Upload 3 files

README.md

@@ -1,535 +1,170 @@
 ---
-title: Copernicus AI - Research-Driven Podcast Generation Platform
-emoji: 🔬
-colorFrom: purple
-colorTo: blue
+title: The Programming Framework
+emoji: 🛠️
+colorFrom: yellow
+colorTo: red
 sdk: static
-pinned: false
+pinned: true
 license: mit
 ---
 
-# 🔬 Copernicus AI - Knowledge Engine for Scientific Discovery
+# 🛠️ The Programming Framework
 
-A collaborative research platform that transforms cutting-edge scientific research into accessible, multi-format tools for collective knowledge exploration. These are research instruments—like microscopes for observing the collective knowledge of humanity—enabling hypothesis formation, testing, and discovery across scientific disciplines.
+A Universal Method for Process Analysis
 
-## Prior Work: CopernicusAI Research Interface
-
-CopernicusAI is an active research prototype exploring AI-generated audio briefings as an interface for assisted scientific research.
-
-The system allows any user to generate, refine, and share AI-generated science podcasts based on structured prompts, enabling rapid orientation to a topic, iterative deepening, and personalized research briefings.
-
-Rather than functioning as a static content platform, CopernicusAI supports collectively generated and shared research artifacts, analogous to community-driven knowledge platforms (e.g., discussion forums), but grounded in scientific sources and metadata-aware workflows.
-
-This work demonstrates technical feasibility for:
-- AI-assisted research briefing and orientation
-- Iterative question refinement via conversational interfaces
-- Integration of text, audio, and metadata in research workflows
-
-## 🎯 Mission & Vision
-
-Inspired by Nicolaus Copernicus who challenged accepted knowledge with evidence and rigorous analysis, **Copernicus AI** creates collaborative research tools that enable collective participation in scientific discovery. These platforms are instruments for exploring humanity's collective knowledge—tools for hypothesis formation, testing, and collaborative research, not just educational content.
-
-Just as a microscope enables observation of the microscopic world, Copernicus AI tools enable observation and exploration of humanity's collective knowledge. Subscribers collaborate to prompt, generate, and refine research content—sharing discoveries publicly or keeping them private. As large language models (LLMs) and AI systems gain unprecedented knowledge, Copernicus AI provides the infrastructure for human-AI collaborative knowledge exploration, with evidence-based truth-seeking as our guiding principle.
-
----
-
-## 🌟 Core Platform Capabilities
-
-### 🎙️ AI-Powered Podcast Generation
-
-**Production-Ready System:**
-- Collaborative platform where subscribers prompt and generate multi-voice AI podcasts (5-10 minutes) synthesizing research from multiple academic sources
-- Subscribers can share their podcasts publicly or keep them private
-- Evidence-based content generation requiring minimum 3 research sources per episode
-- Comprehensive research integration across 8+ academic databases
-- **64 episodes** generated across Biology, Chemistry, Computer Science, Mathematics, and Physics
-- Automated audio synthesis with professional multi-speaker dialogue
-- AI-generated episode thumbnails with scientific visualizations
-- RSS feed distribution compatible with Spotify, Apple Podcasts, Google Podcasts
-
-**Research Integration:**
-- Real-time discovery from PubMed, arXiv, NASA ADS, Zenodo, bioRxiv, CORE, Google Scholar, and News APIs
-- Parallel search across multiple databases for comprehensive coverage
-- Quality scoring and relevance ranking of research sources
-- Paradigm shift identification and interdisciplinary connection analysis
-- Automatic citation extraction and formatting
-- Source validation and authenticity verification
-
-### 🤖 Advanced LLM Integration
-
-**Multi-Model Architecture:**
-- **Google Gemini 3** - Latest research analysis and content generation
-- **OpenAI GPT-4/GPT-3.5** - Content synthesis and quality validation
-- **Anthropic Claude 3** (Sonnet, Haiku via OpenRouter) - Alternative reasoning paths
-- **ElevenLabs TTS** - Multi-voice text-to-speech synthesis
-- Model selection based on task complexity and expertise level
-- Fallback chains for reliability and cost optimization
-
-**Capabilities:**
-- Multi-paper analysis and synthesis
-- Paradigm shift detection in research domains
-- Interdisciplinary connection identification
-- Entity extraction (genes, proteins, chemical compounds, mathematical concepts)
-- Citation tracking and cross-reference analysis
-- Content quality scoring and validation
-
-### 📊 Research Resource Access
-
-**Comprehensive Academic Database Coverage:**
-
-Our research pipeline integrates with **8+ major academic databases**, providing access to:
-
-- **PubMed/NCBI** (~30+ million biomedical papers)
-- **arXiv** (~2+ million preprints in physics, mathematics, CS, quantitative biology)
-- **NASA ADS** (~15+ million astronomy/astrophysics papers)
-- **Zenodo** (100K+ open science datasets and publications)
-- **bioRxiv/medRxiv** (preprints in life sciences)
-- **CORE** (~200+ million open access papers)
-- **Google Scholar** (comprehensive academic search)
-- **News API** (current events and trending research topics)
-- **YouTube Data API** (academic videos, conference talks, lectures)
-
-**Total Access:** **250+ million research papers and academic resources** across all major scientific disciplines.
-
-### 🎙️ Audio and Video Podcast Production
-
-**Operating Audio Podcast System:**
-Full production and distribution platform for subscriber-generated podcasts. Users can prompt, generate, publish, and distribute audio podcasts with RSS feed support for Spotify, Apple Podcasts, and Google Podcasts.
-
-- Multi-voice AI podcast generation
-- Research-driven content creation
-- RSS feed distribution
-- Public and private podcast options
-- Professional audio quality
-
-**Video Production (Future - Phase 2+):**
-
-Advanced video features planned for future development:
-
-**Planned Advanced Features (Phase 2-4):**
-- **Visual Content Integration:**
-  - Automated extraction of figures and diagrams from research papers
-  - Screen capture and processing of academic illustrations
-  - Web scraping from scientific journal websites and preprint servers
-  - JSON database integration for structured visual data
-
-- **Dynamic Visualization Generation:**
-  - On-the-fly scientific animations (molecular structures, data flows, algorithms)
-  - Real-time chart and graph generation from research data
-  - Python-based animations using matplotlib, plotly, mayavi
-  - Mathematical formula rendering (LaTeX → video)
-
-- **External Video Quoting:**
-  - YouTube video segment extraction and integration
-  - Time-stamped video quoting with proper attribution
-  - Educational fair use compliance
-  - Source video discovery during research phase
-
-- **Advanced Composition:**
-  - Multi-layer video composition (background, content, overlays, effects)
-  - Automatic subtitle generation from transcripts
-  - Text overlay system (key concepts, citations, speaker identification)
-  - Professional transitions and effects
-  - Audio-visual synchronization
-
-**See:** [Science Video Database](https://huggingface.co/spaces/garywelz/sciencevideodb) - Companion project for research video content management.
-
-### 📚 Research Papers Metadata Database (Phase 2)
-
-**Planned Implementation:**
-A centralized **metadata repository** (not a file archive) that provides:
-
-- **Structured JSON Objects:** Research paper metadata including:
-  - DOI, arXiv ID, publication information
-  - Abstracts and key findings
-  - Extracted entities (genes, proteins, chemical compounds, equations)
-  - Citation networks and cross-references
-  - Paradigm shift indicators
-  - Interdisciplinary connections
-  - Quality scores and relevance metrics
-
-- **AI-Powered Preprocessing:**
-  - LLM-based entity extraction and annotation
-  - Automatic categorization by discipline and subdomain
-  - Keyword extraction and semantic tagging
-  - Citation tracking and relationship mapping
-  - Quality assessment and validation
-
-- **Integration Features:**
-  - DOI/arXiv ID resolution and metadata enrichment
-  - Cross-reference linking between papers
-  - Podcast-to-paper relationship tracking
-  - Search and query capabilities
-  - API access for programmatic retrieval
-
-**Technical Architecture:**
-- Firestore NoSQL database for flexible JSON storage
-- Google Cloud Functions for automated metadata processing
-- Vertex AI for entity extraction and analysis
-- RESTful API for external access
-
-**Benefits:**
-- Enables rapid research discovery across podcasts
-- Supports knowledge graph construction
-- Facilitates cross-disciplinary pattern recognition
-- Provides foundation for semantic search capabilities
-
----
-
-## 🗄️ System Architecture
-
-### Database Structure (Firestore)
-
-**Collections:**
-- **`subscribers`** - User accounts, preferences, subscription tiers, usage analytics
-- **`podcast_jobs`** - Generated podcasts with full metadata, source papers, engagement metrics
-- **`episodes`** - Published episodes with RSS distribution status
-- **`research_papers`** (Phase 2) - Paper metadata database with AI-extracted entities
-
-### Storage Structure (Google Cloud Storage)
+## 📚 Prior Work & Research Contributions
 
-- **`audio/`** - MP3 podcast files (multi-voice ElevenLabs synthesis)
-- **`videos/`** - MP4 video podcasts (current and future)
-- **`transcripts/`** - Full text transcripts with speaker markers
-- **`descriptions/`** - Markdown descriptions with academic references
-- **`thumbnails/`** - AI-generated episode artwork (DALL-E 3)
-- **`video-assets/`** - Extracted figures, animations, visual content
-- **`glmp-v2/`** - Genome Logic Modeling Project flowcharts (JSON)
+### Overview
+The Programming Framework represents **prior work** that demonstrates a novel methodology for analyzing complex processes by combining Large Language Models (LLMs) with visual flowchart representation. This research establishes a universal, domain-agnostic approach to process analysis that transforms textual descriptions into structured, interactive visualizations.
 
-### Backend Services (Google Cloud Run)
+### 🔬 Research Contributions
+- **Universal Process Analysis:** Domain-agnostic methodology applicable across biology, chemistry, software engineering, business processes, and more
+- **LLM-Powered Extraction:** Automated extraction of process steps, decision points, and logic flows using Google Gemini 2.0 Flash
+- **Structured Visualization:** Mermaid.js-based flowchart generation encoded as JSON for programmatic access and integration
+- **Iterative Refinement:** Systematic approach enabling continuous improvement through visualization and LLM-assisted refinement
 
-**Microservices Architecture:**
-- **Podcast Generation Service** - Orchestrates research, content generation, and media production
-- **Research Pipeline Service** - Multi-API academic search and analysis
-- **Video Generation Service** - Video composition and encoding (Phase 1 complete)
-- **RSS Service** - Feed generation and distribution
-- **Episode Service** - Catalog management and metadata
+### ⚙️ Technical Achievements
+- **Meta-Tool Architecture:** Framework for creating specialized process analysis tools (demonstrated by GLMP)
+- **JSON-Based Storage:** Structured data format enabling version control, cross-referencing, and API integration
+- **Multi-Domain Application:** Successfully applied to biological processes (GLMP), with extensions planned for software, business, and engineering domains
+- **Integration Framework:** Designed for integration with knowledge engines, research databases, and collaborative platforms
 
----
+### 🎯 Position Within CopernicusAI Knowledge Engine
+The Programming Framework serves as the **foundational meta-tool** of the CopernicusAI Knowledge Engine, providing the underlying methodology that enables specialized applications:
 
-## ⚙️ Technology Stack
-
-### AI & Machine Learning
-- **Google Gemini 3** - Latest LLM for research analysis
-- **Google Vertex AI** - Enterprise-scale model deployment and orchestration (used throughout platform)
-- **OpenAI GPT-4/GPT-3.5** - Content synthesis and validation
-- **Anthropic Claude 3** - Alternative reasoning via OpenRouter
-- **ElevenLabs TTS** - Multi-voice text-to-speech synthesis
-- **DALL-E 3** - AI-generated scientific visualizations
-- **Google Cloud Vision API** - Image analysis and quality assessment
-- **Video Intelligence API** - Scene detection and content analysis
-
-### Backend Infrastructure
-- **FastAPI** (Python) - RESTful API framework
-- **Google Cloud Run** - Serverless container deployment
-- **Firestore** - NoSQL document database
-- **Cloud Storage** - Media file storage and CDN
-- **Cloud Functions** - Event-driven processing
-- **Cloud Tasks** - Background job queuing
-- **Secret Manager** - API key and credential management
-
-### Media Processing
-- **FFmpeg** - Video encoding and composition
-- **MoviePy** - Python video editing (planned)
-- **Matplotlib/Plotly** - Scientific visualization (planned)
-- **PyPDF2/pdfplumber** - PDF processing (planned)
-
-### Frontend
-- **Next.js 15.5.7** - React framework
-- **Alpine.js** - Lightweight reactive UI
-- **Tailwind CSS** - Utility-first styling
-- **Vercel** - Frontend hosting and deployment
+- **GLMP (Genome Logic Modeling Project)** - First specialized application demonstrating biological process visualization
+- **Copernicus AI** - Main knowledge engine integrating Framework outputs with AI podcasts and research synthesis
+- **Research Papers Metadata Database** - Planned integration for linking processes to source literature
+- **Science Video Database** - Potential integration for multi-modal process explanations
 
----
+This work establishes a proof-of-concept for AI-assisted process analysis, demonstrating how LLMs can systematically extract and visualize complex logic from textual sources across diverse domains.
 
-## 📈 Platform Capabilities
+## 🎯 Overview
 
-### Research Coverage
-- **250+ million research papers** accessible through integrated APIs
-- **8+ academic databases** integrated with parallel search
-- **Minimum 3 sources** required per episode for quality assurance
-- **Multi-paper analysis** for comprehensive coverage
+The Programming Framework is a **meta-tool**—a tool for creating tools. It provides a systematic method for analyzing any complex process by combining the analytical power of Large Language Models with the clarity of visual flowcharts.
 
-### Platform Features
-- **Subscriber-driven content generation** - Users prompt and create podcasts
-- **RSS feed distribution** to major podcast platforms
-- **Public and private podcast options** - Share discoveries or keep them private
+## 💡 The Core Idea
 
----
+**Problem:** Complex processes are difficult to understand because they involve many steps, decision points, and interactions. Traditional text descriptions are hard to follow.
 
-## 🔗 Live Platform & Resources
+**Solution:** Use LLMs to extract process logic from literature, then encode it as Mermaid flowcharts stored in JSON. Result: Clear, interactive visualizations that reveal hidden patterns and enable systematic analysis.
 
-### Production Deployment
-- 🏠 **[Homepage - Browse Podcasts](https://www.copernicusai.fyi)** - Public podcast catalog
-- 📊 **[Creator Dashboard](https://www.copernicusai.fyi/subscriber-dashboard.html)** - Subscriber interface
-- 📡 **[RSS Feed](https://storage.googleapis.com/regal-scholar-453620-r7-podcast-storage/feeds/copernicus-mvp-rss-feed.xml)** - Podcast distribution feed
+## ⚙️ How It Works
 
-## 🧩 CopernicusAI Knowledge Engine Components
+1. **Input Process** - Provide scientific papers, documentation, or process descriptions
+2. **LLM Analysis** - AI extracts steps, decisions, branches, and logic flow
+3. **Generate Flowchart** - Create Mermaid diagram encoded as JSON structure
+4. **Visualize & Iterate** - Interactive flowchart reveals insights and enables refinement
 
-The CopernicusAI Knowledge Engine is an integrated ecosystem of research and collaboration tools. Currently, the platform includes five core components, with additional tools, databases, and collaboration features planned for future development:
+## 🌍 Core Principles
 
-### Core Components
+### Domain Agnostic
+Works across any field: biology, chemistry, software engineering, business processes, legal workflows, manufacturing, and beyond.
 
-1. **🔬 Copernicus AI (This Platform)** - Core synthesis and distribution component
-   - AI-powered research synthesis and podcast generation
-   - Multi-API research integration (250+ million papers)
-   - Subscriber-driven content creation and sharing
-   - RSS feed distribution and platform management
+### Iterative Refinement
+Start with rough analysis, visualize, identify gaps, refine with LLM, repeat until the process logic is crystal clear.
 
-2. **🛠️ Programming Framework** - Foundational meta-tool
-   - Universal method for process analysis across any discipline
-   - LLM-powered extraction and Mermaid visualization
-   - Domain-agnostic methodology for complex process analysis
-   - [Explore Framework →](https://huggingface.co/spaces/garywelz/programming_framework)
+### Structured Data
+JSON storage enables programmatic access, version control, cross-referencing, and integration with other tools and databases.
 
-3. **🧬 GLMP - Genome Logic Modeling Project** - Specialized biological application
-   - First application of Programming Framework to biology
-   - 50+ biological processes visualized as interactive flowcharts
-   - JSON-based structured data in Google Cloud Storage
-   - [Explore GLMP →](https://huggingface.co/spaces/garywelz/glmp)
+## 🚀 Applications
 
-4. **📚 Research Paper Metadata Database** - Core data infrastructure
-   - Centralized metadata repository for scientific research papers
-   - AI-powered preprocessing and entity extraction
-   - Citation network analysis and relationship mapping
-   - Foundation for knowledge graph construction
-   - [Explore Metadata Database →](https://huggingface.co/spaces/garywelz/metadata_database)
+### 🧬 GLMP - Genome Logic Modeling (Live)
+First specialized application: visualizing biochemical processes like DNA replication, metabolic pathways, and cell signaling.
+- [Explore GLMP →](https://huggingface.co/spaces/garywelz/glmp)
 
-5. **🎬 Science Video Database** - Multi-modal content component
-   - Curated searchable database of scientific video content
-   - Transcript-based search across multiple disciplines
-   - Integration with YouTube and other video sources
-   - [Explore Video Database →](https://huggingface.co/spaces/garywelz/sciencevideodb)
-   - [Live Demo →](https://scienceviddb-web-204731194849.us-central1.run.app/)
+## 📚 Process Diagram Collections
 
-### Future Components
+The Programming Framework has been applied across multiple scientific disciplines. Explore interactive flowchart collections organized by domain:
 
-The Knowledge Engine is designed to grow and evolve. Additional tools, databases, and collaboration components will be added as the project develops, expanding capabilities for AI-assisted scientific research and knowledge discovery.
+### 🧬 Biology
+- [Biology Processes Collection](https://huggingface.co/spaces/garywelz/programming_framework/blob/main/biology_processes.html) - Links to the Genome Logic Modeling Project (GLMP)
 
----
+### ⚗️ Chemistry
+- [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
 
-## 🔌 API Documentation
+### 🔢 Mathematics
+- [Mathematics Processes Collection](https://huggingface.co/spaces/garywelz/programming_framework/blob/main/mathematics_processes.html) - Overview of mathematics process diagrams
 
-**Base URL:** `https://copernicus-podcast-api-phzp4ie2sq-uc.a.run.app`
+### ⚛️ Physics
+- [Physics Processes Collection](https://huggingface.co/spaces/garywelz/programming_framework/blob/main/physics_processes.html) - Overview of physics process diagrams
 
-### Podcast Generation Endpoints
-- `POST /generate-podcast-with-subscriber` - Generate new podcast from research topic
-- `GET /api/subscribers/podcasts/{id}` - Retrieve podcast details
-- `POST /api/subscribers/podcasts/submit-to-rss` - Publish to RSS feed
+### 💻 Computer Science
+- [Computer Science Index](https://huggingface.co/spaces/garywelz/programming_framework/blob/main/computer_science_index.html) - Main index for computer science processes
 
-### Research Endpoints
-- `POST /api/papers/upload` - Upload paper metadata (Phase 2)
-- `GET /api/papers/{paper_id}` - Retrieve paper metadata
-- `POST /api/papers/query` - Query papers by discipline, keywords
-- `POST /api/papers/{id}/link-podcast/{id}` - Link paper to podcast
+## 🔧 Technical Architecture
 
-### Admin Endpoints
-- `GET /api/admin/subscribers` - List all subscribers and statistics
-- `POST /api/admin/podcasts/fix-missing-titles` - Content maintenance
-- `GET /api/admin/podcasts/catalog` - Full podcast catalog
+### LLM Integration
+- Google Gemini 2.0 Flash for analysis
+- Vertex AI for enterprise deployment
+- Custom prompts for process extraction
+- Structured JSON output formatting
 
----
+### Visualization Stack
+- Mermaid.js for flowchart rendering
+- JSON schema for data validation
+- Interactive SVG output
+- Export to PNG/PDF supported
 
-## 🚀 Development Roadmap
-
-### ✅ Phase 1: Core Platform (Complete)
-- Multi-API research integration
-- AI podcast generation with multi-voice synthesis
-- RSS feed distribution
-- Subscriber platform
-- Basic video generation (static)
-
-### 🔄 Phase 2: Content Enhancement (In Progress)
-- **Research Papers Metadata Database** - JSON-based metadata repository
-- **Visual Content Extraction** - Figures from papers, web scraping
-- **YouTube Video Quoting** - External video integration with attribution
-- **Advanced Video Features** - Multi-layer composition, animations
-
-### 📋 Phase 3: Advanced Visualizations (Planned)
-- Scientific animation generation (matplotlib, plotly)
-- Real-time data visualization
-- Mathematical formula rendering
-- Dynamic graph and network visualizations
-
-### 🎯 Phase 4: Knowledge Integration (Planned)
-- Knowledge graph construction
-- Semantic search capabilities
-- Cross-disciplinary pattern discovery
-- AI-powered content recommendations
+### Data Storage
+- Google Cloud Storage for JSON files
+- Firestore for metadata indexing
+- Version control with Git
+- Cross-referencing with papers database
 
----
+### Integration Points
+- GLMP specialized collections
+- Copernicus AI knowledge graph
+- Research papers database
+- API endpoints for programmatic access
 
-## 🔬 Collaborative Research Tools
+### How to Cite This Work
 
-**These platforms enable collective participation and collaboration across diverse user communities:**
+Welz, G. (2024–2025). *The Programming Framework: A Universal Method for Process Analysis*.
+Hugging Face Spaces. https://huggingface.co/spaces/garywelz/programming_framework
 
-- **Researchers** - Tools for hypothesis formation and testing, rapid synthesis of cross-disciplinary findings
-- **Collaborators** - Collective knowledge exploration and refinement
-- **Subscribers** - Prompt, generate, and share podcasts (public or private)
-- **Community** - User suggestions, comments, and collaborative flowchart improvement (GLMP)
+Welz, G. (2024). *From Inspiration to AI: Biology as Visual Programming*. Medium. 
+https://medium.com/@garywelz_47126/from-inspiration-to-ai-biology-as-visual-programming-520ee523029a
 
-**Key Innovations:**
-- **Multi-Source Validation** - Requires minimum 3 research sources per episode
-- **Evidence-Based Generation** - No content generated without research backing
-- **Paradigm Shift Detection** - Identifies revolutionary vs. incremental research
-- **Interdisciplinary Connections** - Reveals cross-domain insights
-- **Collaborative Participation** - User-driven content generation and sharing
-- **Reproducibility** - Full citation tracking and source attribution
+This project serves as a foundational meta-tool for AI-assisted process analysis, enabling systematic extraction and visualization of complex logic from textual sources across diverse scientific and technical domains.
 
-> *Like a microscope enables observation of the microscopic world, these tools enable observation and exploration of humanity's collective knowledge.*
+The Programming Framework is designed as infrastructure for AI-assisted science, providing a universal methodology that can be specialized for domain-specific applications.
 
----
+## 🔗 Related Projects
 
-## 📚 Prior Work & Research Contributions
+### 🧬 GLMP - Genome Logic Modeling
+First specialized application of the Programming Framework to biochemical processes. 50+ biological pathways visualized.
+- [Visit GLMP →](https://huggingface.co/spaces/garywelz/glmp)
 
-### Overview
-This platform represents **prior work** that demonstrates foundational research and development achievements in AI-powered scientific knowledge synthesis, collaborative research tools, and multi-modal content generation. These contributions establish the technical foundation and proof-of-concept for the broader **CopernicusAI Knowledge Engine** initiative.
-
-### Research Contributions
-
-**1. AI-Powered Research Synthesis System**
-- Developed and deployed a production-ready system for multi-source research synthesis using LLMs
-- Demonstrated integration of 8+ academic databases (250+ million papers) with parallel search capabilities
-- Implemented evidence-based content generation requiring minimum 3 research sources per output
-- Achieved operational deployment with 64+ generated podcast episodes across 5 scientific disciplines
-
-**2. Multi-Model LLM Architecture**
-- Designed and implemented intelligent model selection framework using Google Gemini 3, OpenAI GPT-4, and Anthropic Claude 3
-- Developed fallback chains for reliability and cost optimization
-- Demonstrated paradigm shift detection and interdisciplinary connection identification in research domains
-- Implemented entity extraction (genes, proteins, chemical compounds, mathematical concepts) from research literature
-
-**3. Collaborative Research Platform Infrastructure**
-- Built subscriber-driven content generation system enabling public/private research sharing
-- Implemented RSS feed distribution compatible with major podcast platforms
-- Developed microservices architecture on Google Cloud Run with Firestore and Cloud Storage
-- Created RESTful API framework for programmatic access to research synthesis capabilities
-
-**4. Integration with Knowledge Engine Components**
-- Established integration pathways with GLMP (Genome Logic Modeling Project) for biological process visualization
-- Designed architecture for Research Papers Metadata Database (Phase 2)
-- Planned integration with Science Video Database for multi-modal content
-- Created framework for Programming Framework integration across disciplines
-
-### Technical Achievements
-
-**Production Deployment:**
-- Live platform: https://www.copernicusai.fyi
-- Operational API: https://copernicus-podcast-api-phzp4ie2sq-uc.a.run.app
-- RSS feed distribution: Active and functional
-- Multi-voice audio synthesis: ElevenLabs TTS integration operational
-
-**Research Infrastructure:**
-- 250+ million research papers accessible via integrated APIs
-- 8+ academic database integrations (PubMed, arXiv, NASA ADS, Zenodo, bioRxiv, CORE, Google Scholar, News API)
-- Automated citation extraction and formatting
-- Quality scoring and relevance ranking systems
-
-**Scalability & Architecture:**
-- Serverless microservices architecture (Google Cloud Run)
-- NoSQL database (Firestore) for flexible metadata storage
-- Cloud Storage for media files and structured data
-- Event-driven processing with Cloud Functions and Cloud Tasks
-
-### Position Within CopernicusAI Knowledge Engine
-
-This platform serves as the **core synthesis and distribution component** of the CopernicusAI Knowledge Engine. The Knowledge Engine is an integrated ecosystem of research and collaboration tools that work together to assist scientists in their workflow, from research discovery through knowledge synthesis to multi-format content generation.
-
-**Current Components:**
-1. **Copernicus AI** (This platform) - Core synthesis and distribution component for AI-powered research synthesis and podcast generation
-2. **Programming Framework** - Foundational meta-tool providing universal process analysis methodology
-3. **GLMP (Genome Logic Modeling Project)** - Specialized biological application demonstrating domain-specific use of the Programming Framework
-4. **Research Paper Metadata Database** - Core data infrastructure providing structured metadata and citation networks
-5. **Science Video Database** - Multi-modal content component enabling video-based learning and research discovery
-
-**Future Development:**
-The Knowledge Engine is designed to grow and evolve. Additional tools, databases, and collaboration components will be added as the project develops, expanding capabilities for AI-assisted scientific research and knowledge discovery.
-
-### Academic & Research Impact
-
-**Publications & Presentations:**
-- Platform architecture and methodology suitable for academic publication
-- Open-source components available for research community use
-- Publicly accessible research tools demonstrating AI-human collaboration in scientific knowledge synthesis
-
-**Research Applications:**
-- Supports hypothesis formation and testing through rapid multi-source synthesis
-- Enables cross-disciplinary pattern recognition and connection identification
-- Facilitates reproducible research communication with full citation tracking
-- Provides infrastructure for collaborative knowledge exploration
-
-**Educational Contributions:**
-- 64+ research-driven podcast episodes across Biology, Chemistry, Computer Science, Mathematics, and Physics
-- Evidence-based content requiring minimum 3 academic sources
-- Public and private sharing options for research dissemination
-- Integration with major podcast platforms for broad accessibility
-
-### Citation Information
-
-**For Grant Proposals:**
-When citing this work as prior research, please reference:
-
-- **Platform Name:** Copernicus AI - Knowledge Engine for Scientific Discovery
-- **URL:** https://huggingface.co/spaces/garywelz/copernicusai
-- **Live Platform:** https://www.copernicusai.fyi
-- **Primary Developer:** Gary Welz
-- **Year:** 2024-2025
-- **License:** MIT
-
-**Suggested Citation Format:**
-```
-Welz, G. (2025). Copernicus AI: Knowledge Engine for Scientific Discovery. 
-Hugging Face Space. https://huggingface.co/spaces/garywelz/copernicusai
-```
-
-## 🌐 Grant Support & Collaboration
-
-**Grant Applications Supported:**
-This platform is designed to support grant applications to:
-- **NSF (National Science Foundation)** - Science education and research infrastructure
-- **DOE (Department of Energy)** - Scientific computing and data science
-- **SAIR Foundation** - AI research and development initiatives
-
-**Research Contributions:**
-- Open-source components and methodologies
-- Publicly accessible research tools
-- Educational content for broader scientific literacy
-- Infrastructure for reproducible research communication
-
-**Collaboration Opportunities:**
-- Integration with academic institutions
-- Partnership with research organizations
-- Open data initiatives
-- Educational program development
+### 🔬 Copernicus AI
+Knowledge engine integrating the Programming Framework with AI podcasts, research papers, and knowledge graph for scientific discovery.
+- [Visit Copernicus AI →](https://huggingface.co/spaces/garywelz/copernicusai)
 
----
+## 🎨 Interactive Demo
 
-## How to Cite This Work
+The space includes interactive examples showing the framework applied to:
+- Scientific Method
+- Software Deployment Pipeline
+- Customer Support Workflow
+- Research Paper Publication
 
-Welz, G. (2024–2025). *CopernicusAI: AI-Generated Audio Briefings as a Research Interface*.
-Hugging Face Spaces. https://huggingface.co/spaces/garywelz/copernicusai
+Each example demonstrates how LLMs extract process logic and encode it as visual flowcharts.
 
----
+## 💻 Technology Stack
 
-## 📄 License & Attribution
+- **LLM**: Google Gemini 2.0 Flash, Vertex AI
+- **Visualization**: Mermaid.js
+- **Storage**: Google Cloud Storage, Firestore
+- **Format**: JSON with Mermaid syntax
+- **Frontend**: Static HTML + Tailwind CSS
 
-**License:** MIT
+## 🌟 Vision
 
-**Attributions:**
-- Built with Google Cloud Platform, Gemini AI, OpenAI, Anthropic Claude, and ElevenLabs
-- Research data from PubMed, arXiv, NASA ADS, Zenodo, bioRxiv, CORE, and Google Scholar
-- Academic paper metadata from respective publishers
+As AI systems become more capable of understanding complex processes, the Programming Framework provides the bridge between human comprehension and machine analysis. It's a tool for truth-seeking—transforming complexity into clarity.
 
 ---
 
-## 📧 Contact & Support
-
-For questions, collaboration inquiries, or grant application support:
-- **Hugging Face Space:** [https://huggingface.co/spaces/garywelz/copernicusai](https://huggingface.co/spaces/garywelz/copernicusai)
-- **Platform:** [https://www.copernicusai.fyi](https://www.copernicusai.fyi)
-
----
+**A Universal Method for Process Analysis**
 
-**© 2025 Copernicus AI. All rights reserved.**
+© 2025 Gary Welz. All rights reserved.
 
-*Advancing scientific knowledge through AI-powered research communication and discovery.*

index.html

@@ -3,11 +3,12 @@
 <head>
     <meta charset="UTF-8">
     <meta name="viewport" content="width=device-width, initial-scale=1.0">
-    <title>Copernicus AI - Research-Driven Podcast Generation Platform</title>
+    <title>The Programming Framework - Universal Process Analysis</title>
     <script src="https://cdn.tailwindcss.com"></script>
+    <script src="https://cdn.jsdelivr.net/npm/mermaid/dist/mermaid.min.js"></script>
     <style>
         .gradient-bg {
-            background: linear-gradient(135deg, #667eea 0%, #764ba2 100%);
+            background: linear-gradient(135deg, #f59e0b 0%, #d97706 100%);
         }
         .card-hover {
             transition: transform 0.3s ease, box-shadow 0.3s ease;
@@ -16,13 +17,6 @@
             transform: translateY(-4px);
             box-shadow: 0 20px 40px rgba(0,0,0,0.15);
         }
-        .stat-number {
-            font-size: 2.5rem;
-            font-weight: bold;
-            background: linear-gradient(135deg, #667eea 0%, #764ba2 100%);
-            -webkit-background-clip: text;
-            -webkit-text-fill-color: transparent;
-        }
     </style>
 </head>
 <body class="bg-gray-50">
@@ -30,659 +24,507 @@
     <header class="gradient-bg text-white">
         <div class="max-w-7xl mx-auto px-4 sm:px-6 lg:px-8 py-16">
             <div class="text-center">
-                <div class="text-6xl mb-4">🔬</div>
-                <h1 class="text-5xl font-bold mb-4">Copernicus AI</h1>
-                <p class="text-xl opacity-90 mb-6">Knowledge Engine for Scientific Discovery</p>
-                <p class="text-lg opacity-75 max-w-4xl mx-auto">
-                    A collaborative research platform that transforms cutting-edge scientific research into accessible, 
-                    multi-format tools for collective knowledge exploration. These are research instruments—like microscopes 
-                    for observing the collective knowledge of humanity—enabling hypothesis formation, testing, and discovery 
-                    across scientific disciplines.
+                <div class="text-6xl mb-4">🛠️</div>
+                <h1 class="text-5xl font-bold mb-4">The Programming Framework</h1>
+                <p class="text-xl opacity-90 mb-6">A Universal Method for Process Analysis</p>
+                <p class="text-lg opacity-75 max-w-3xl mx-auto">
+                    Combining Large Language Models with Mermaid visualization to dissect and understand 
+                    complex processes across any discipline—from biology to business, physics to psychology.
                 </p>
             </div>
         </div>
     </header>
 
-    <!-- Prior Work: CopernicusAI Research Interface -->
+    <!-- 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-purple-50 to-blue-50 rounded-xl shadow-lg p-8 mb-8">
-            <h2 class="text-3xl font-bold text-gray-900 mb-4">Prior Work: CopernicusAI Research Interface</h2>
-            <p class="text-lg text-gray-700 leading-relaxed mb-4">
-                CopernicusAI is an active research prototype exploring AI-generated audio briefings as an interface for assisted scientific research.
-            </p>
-            <p class="text-gray-700 mb-4">
-                The system allows any user to generate, refine, and share AI-generated science podcasts based on structured prompts, enabling rapid orientation to a topic, iterative deepening, and personalized research briefings.
-            </p>
-            <p class="text-gray-700 mb-4">
-                Rather than functioning as a static content platform, CopernicusAI supports collectively generated and shared research artifacts, analogous to community-driven knowledge platforms (e.g., discussion forums), but grounded in scientific sources and metadata-aware workflows.
-            </p>
-            <div class="bg-white rounded-lg p-4 mt-4">
-                <h3 class="font-semibold text-gray-900 mb-2">This work demonstrates technical feasibility for:</h3>
-                <ul class="text-gray-700 space-y-1">
-                    <li>• AI-assisted research briefing and orientation</li>
-                    <li>• Iterative question refinement via conversational interfaces</li>
-                    <li>• Integration of text, audio, and metadata in research workflows</li>
-                </ul>
+        <div class="bg-gradient-to-r from-orange-50 to-yellow-50 rounded-xl shadow-lg p-8 mb-8">
+            <h2 class="text-3xl font-bold text-gray-900 mb-6">📚 Prior Work & Research Contributions</h2>
+            
+            <div class="bg-white rounded-lg p-6 mb-6">
+                <h3 class="text-xl font-semibold text-gray-900 mb-4">Overview</h3>
+                <p class="text-gray-700 mb-4">
+                    The Programming Framework represents <strong>prior work</strong> that demonstrates a novel methodology for analyzing complex processes by combining Large Language Models (LLMs) with visual flowchart representation. This research establishes a universal, domain-agnostic approach to process analysis that transforms textual descriptions into structured, interactive visualizations.
+                </p>
             </div>
-        </div>
-    </section>
 
-    <!-- Mission & Vision -->
-    <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">
-            <h2 class="text-3xl font-bold text-gray-900 mb-4">🎯 Mission & Vision</h2>
-            <p class="text-lg text-gray-700 leading-relaxed mb-4">
-                Inspired by Nicolaus Copernicus who challenged accepted knowledge with evidence and rigorous analysis, 
-                <strong>Copernicus AI</strong> creates collaborative research tools that enable collective participation in 
-                scientific discovery. These platforms are instruments for exploring humanity's collective knowledge—tools for 
-                hypothesis formation, testing, and collaborative research, not just educational content.
-            </p>
-            <p class="text-gray-600">
-                Just as a microscope enables observation of the microscopic world, Copernicus AI tools enable observation and 
-                exploration of humanity's collective knowledge. Subscribers collaborate to prompt, generate, and refine research 
-                content—sharing discoveries publicly or keeping them private. As large language models (LLMs) and AI systems 
-                gain unprecedented knowledge, Copernicus AI provides the infrastructure for human-AI collaborative knowledge 
-                exploration, with evidence-based truth-seeking as our guiding principle.
-            </p>
-        </div>
-    </section>
-
-    <!-- Knowledge Engine Ecosystem -->
-    <section class="max-w-7xl mx-auto px-4 sm:px-6 lg:px-8 py-8">
-        <div class="bg-gradient-to-r from-purple-50 to-indigo-50 rounded-xl shadow-lg p-8 mb-8">
-            <h2 class="text-3xl font-bold text-gray-900 mb-6 text-center">🧩 CopernicusAI Knowledge Engine</h2>
-            <p class="text-lg text-gray-700 mb-6 text-center max-w-4xl mx-auto">
-                An integrated ecosystem of research and collaboration tools designed to assist scientists in their workflow, 
-                from research discovery through knowledge synthesis to multi-format content generation.
-            </p>
-            
-            <div class="grid md:grid-cols-2 lg:grid-cols-3 gap-6 mb-6">
-                <div class="bg-white rounded-lg p-6 card-hover">
-                    <div class="text-3xl mb-3">🔬</div>
-                    <h3 class="text-lg font-semibold text-gray-900 mb-2">Copernicus AI</h3>
-                    <p class="text-sm text-gray-600 mb-3">Core synthesis & distribution platform for AI-powered research and podcast generation</p>
-                    <p class="text-xs text-gray-500 italic">This platform</p>
-                </div>
-                
-                <div class="bg-white rounded-lg p-6 card-hover">
-                    <div class="text-3xl mb-3">🛠️</div>
-                    <h3 class="text-lg font-semibold text-gray-900 mb-2">Programming Framework</h3>
-                    <p class="text-sm text-gray-600 mb-3">Foundational meta-tool for universal process analysis across disciplines</p>
-                    <a href="https://huggingface.co/spaces/garywelz/programming_framework" target="_blank" class="text-xs text-blue-600 hover:underline">Explore →</a>
-                </div>
-                
-                <div class="bg-white rounded-lg p-6 card-hover">
-                    <div class="text-3xl mb-3">🧬</div>
-                    <h3 class="text-lg font-semibold text-gray-900 mb-2">GLMP</h3>
-                    <p class="text-sm text-gray-600 mb-3">Biological process visualization - 50+ processes mapped</p>
-                    <a href="https://huggingface.co/spaces/garywelz/glmp" target="_blank" class="text-xs text-blue-600 hover:underline">Explore →</a>
-                </div>
-                
-                <div class="bg-white rounded-lg p-6 card-hover">
-                    <div class="text-3xl mb-3">📚</div>
-                    <h3 class="text-lg font-semibold text-gray-900 mb-2">Metadata Database</h3>
-                    <p class="text-sm text-gray-600 mb-3">Core data infrastructure for research paper metadata and citation networks</p>
-                    <a href="https://huggingface.co/spaces/garywelz/metadata_database" target="_blank" class="text-xs text-blue-600 hover:underline">Explore →</a>
+            <div class="grid md:grid-cols-2 gap-6 mb-6">
+                <div class="bg-white rounded-lg p-6">
+                    <h3 class="text-lg font-semibold text-gray-900 mb-3">🔬 Research Contributions</h3>
+                    <ul class="text-sm text-gray-700 space-y-2">
+                        <li>• <strong>Universal Process Analysis:</strong> Domain-agnostic methodology applicable across multiple fields</li>
+                        <li>• <strong>LLM-Powered Extraction:</strong> Automated extraction using Google Gemini 2.0 Flash</li>
+                        <li>• <strong>Structured Visualization:</strong> Mermaid.js-based flowchart generation encoded as JSON</li>
+                        <li>• <strong>Iterative Refinement:</strong> Systematic approach enabling continuous improvement</li>
+                    </ul>
                 </div>
                 
-                <div class="bg-white rounded-lg p-6 card-hover">
-                    <div class="text-3xl mb-3">🎬</div>
-                    <h3 class="text-lg font-semibold text-gray-900 mb-2">Video Database</h3>
-                    <p class="text-sm text-gray-600 mb-3">Multi-modal content with transcript-based search for scientific videos</p>
-                    <a href="https://huggingface.co/spaces/garywelz/sciencevideodb" target="_blank" class="text-xs text-blue-600 hover:underline">Explore →</a>
+                <div class="bg-white rounded-lg p-6">
+                    <h3 class="text-lg font-semibold text-gray-900 mb-3">⚙️ Technical Achievements</h3>
+                    <ul class="text-sm text-gray-700 space-y-2">
+                        <li>• <strong>Meta-Tool Architecture:</strong> Framework for creating specialized analysis tools</li>
+                        <li>• <strong>JSON-Based Storage:</strong> Structured format enabling version control and API integration</li>
+                        <li>• <strong>Multi-Domain Application:</strong> Successfully applied to biological processes (GLMP)</li>
+                        <li>• <strong>Integration Framework:</strong> Designed for knowledge engines and collaborative platforms</li>
+                    </ul>
                 </div>
-                
-                <div class="bg-white rounded-lg p-6 card-hover border-2 border-dashed border-gray-300">
-                    <div class="text-3xl mb-3 opacity-50">➕</div>
-                    <h3 class="text-lg font-semibold text-gray-900 mb-2">Future Components</h3>
-                    <p class="text-sm text-gray-600 mb-3">Additional tools, databases, and collaboration features will be added as the project develops</p>
+            </div>
+
+            <div class="bg-white rounded-lg p-6">
+                <h3 class="text-lg font-semibold text-gray-900 mb-3">🎯 Position Within CopernicusAI Knowledge Engine</h3>
+                <p class="text-gray-700 mb-3">
+                    The Programming Framework serves as the <strong>foundational meta-tool</strong> of the CopernicusAI Knowledge Engine, providing the underlying methodology that enables specialized applications:
+                </p>
+                <div class="grid md:grid-cols-2 gap-4 text-sm mb-3">
+                    <ul class="text-gray-700 space-y-1">
+                        <li>• GLMP (Genome Logic Modeling Project)</li>
+                        <li>• Copernicus AI (main knowledge engine)</li>
+                        <li>• Research Papers Metadata Database</li>
+                    </ul>
+                    <ul class="text-gray-700 space-y-1">
+                        <li>• Science Video Database</li>
+                        <li>• Multi-domain process analysis</li>
+                    </ul>
                 </div>
+                <p class="text-gray-600 text-sm italic">
+                    This work establishes a proof-of-concept for AI-assisted process analysis, demonstrating how LLMs can systematically extract and visualize complex logic from textual sources across diverse domains.
+                </p>
             </div>
         </div>
     </section>
 
-    <!-- Key Statistics -->
-    <section class="max-w-7xl mx-auto px-4 sm:px-6 lg:px-8 py-8">
-        <div class="grid md:grid-cols-2 gap-6 mb-12">
-            <div class="bg-white rounded-lg shadow-md p-6 text-center">
-                <div class="stat-number mb-2">250+</div>
-                <div class="text-gray-600 font-semibold">Million Papers</div>
-                <div class="text-sm text-gray-500 mt-1">Accessible via APIs</div>
+    <!-- Key Stats -->
+    <section class="max-w-7xl mx-auto px-4 sm:px-6 lg:px-8 -mt-8">
+        <div class="grid md:grid-cols-4 gap-4">
+            <div class="bg-white rounded-lg shadow-lg p-6 text-center">
+                <div class="text-3xl font-bold text-orange-600">Any</div>
+                <div class="text-sm text-gray-600">Discipline</div>
             </div>
-            <div class="bg-white rounded-lg shadow-md p-6 text-center">
-                <div class="stat-number mb-2">8+</div>
-                <div class="text-gray-600 font-semibold">Academic Databases</div>
-                <div class="text-sm text-gray-500 mt-1">Integrated research sources</div>
+            <div class="bg-white rounded-lg shadow-lg p-6 text-center">
+                <div class="text-3xl font-bold text-blue-600">LLM</div>
+                <div class="text-sm text-gray-600">Powered</div>
             </div>
-        </div>
-    </section>
-
-    <!-- Core Platform Capabilities -->
-    <section class="max-w-7xl mx-auto px-4 sm:px-6 lg:px-8 py-8">
-        <h2 class="text-3xl font-bold text-gray-900 mb-8 text-center">🌟 Core Platform Capabilities</h2>
-        
-        <div class="space-y-8">
-            <!-- AI Podcast Generation -->
-            <div class="bg-white rounded-xl shadow-lg p-8">
-                <div class="flex items-start mb-4">
-                    <span class="text-4xl mr-4">🎙️</span>
-                    <div class="flex-1">
-                        <h3 class="text-2xl font-bold text-gray-900 mb-3">AI-Powered Podcast Generation</h3>
-                        <p class="text-gray-600 mb-4">
-                            Collaborative research platform where subscribers prompt and generate multi-voice AI podcasts 
-                            (5-10 minutes) synthesizing research from multiple academic sources. Subscribers can share their 
-                            podcasts publicly or keep them private. Evidence-based content generation requiring minimum 3 
-                            research sources per episode.
-                        </p>
-                        <div class="grid md:grid-cols-2 gap-4 mt-4">
-                            <div>
-                                <h4 class="font-semibold text-gray-800 mb-2">Key Features:</h4>
-                                <ul class="text-sm text-gray-600 space-y-1">
-                                    <li>✓ Comprehensive research integration (8+ databases)</li>
-                                    <li>✓ Professional multi-speaker dialogue</li>
-                                    <li>✓ AI-generated scientific visualizations</li>
-                                    <li>✓ RSS feed distribution</li>
-                                    <li>✓ Quality scoring & relevance ranking</li>
-                                    <li>✓ Paradigm shift identification</li>
-                                </ul>
-                            </div>
-                            <div>
-                                <h4 class="font-semibold text-gray-800 mb-2">Research Integration:</h4>
-                                <ul class="text-sm text-gray-600 space-y-1">
-                                    <li>✓ Real-time discovery from 8+ APIs</li>
-                                    <li>✓ Parallel search across databases</li>
-                                    <li>✓ Automatic citation extraction</li>
-                                    <li>✓ Source validation & verification</li>
-                                    <li>✓ Interdisciplinary connection analysis</li>
-                                </ul>
-                            </div>
-                        </div>
-                    </div>
-                </div>
+            <div class="bg-white rounded-lg shadow-lg p-6 text-center">
+                <div class="text-3xl font-bold text-green-600">Visual</div>
+                <div class="text-sm text-gray-600">Flowcharts</div>
             </div>
-
-            <!-- LLM Integration -->
-            <div class="bg-white rounded-xl shadow-lg p-8">
-                <div class="flex items-start mb-4">
-                    <span class="text-4xl mr-4">🤖</span>
-                    <div class="flex-1">
-                        <h3 class="text-2xl font-bold text-gray-900 mb-3">Advanced LLM Integration</h3>
-                        <p class="text-gray-600 mb-4">Multi-model architecture with intelligent model selection:</p>
-                        <div class="grid md:grid-cols-2 gap-4">
-                            <div>
-                                <h4 class="font-semibold text-gray-800 mb-2">Primary Models:</h4>
-                                <ul class="text-sm text-gray-600 space-y-1">
-                                    <li>• <strong>Google Gemini 3</strong> - Latest research analysis and content generation</li>
-                                    <li>• <strong>OpenAI GPT-4/GPT-3.5</strong> - Content synthesis and quality validation</li>
-                                    <li>• <strong>Anthropic Claude 3</strong> (Sonnet, Haiku) - Alternative reasoning paths</li>
-                                    <li>• <strong>ElevenLabs TTS</strong> - Multi-voice text-to-speech synthesis</li>
-                                </ul>
-                            </div>
-                            <div>
-                                <h4 class="font-semibold text-gray-800 mb-2">Capabilities:</h4>
-                                <ul class="text-sm text-gray-600 space-y-1">
-                                    <li>• Multi-paper analysis & synthesis</li>
-                                    <li>• Paradigm shift detection</li>
-                                    <li>• Entity extraction (genes, proteins, compounds)</li>
-                                    <li>• Citation tracking & cross-references</li>
-                                    <li>• Content quality scoring</li>
-                                </ul>
-                            </div>
-                        </div>
-                    </div>
-                </div>
+            <div class="bg-white rounded-lg shadow-lg p-6 text-center">
+                <div class="text-3xl font-bold text-purple-600">JSON</div>
+                <div class="text-sm text-gray-600">Structured Data</div>
             </div>
+        </div>
+    </section>
 
-            <!-- Research Resources -->
-            <div class="bg-white rounded-xl shadow-lg p-8">
-                <div class="flex items-start mb-4">
-                    <span class="text-4xl mr-4">📊</span>
-                    <div class="flex-1">
-                        <h3 class="text-2xl font-bold text-gray-900 mb-3">Research Resource Access</h3>
-                        <p class="text-gray-600 mb-4">
-                            Comprehensive academic database coverage with <strong>250+ million research papers</strong> accessible 
-                            through integrated APIs.
-                        </p>
-                        <div class="grid md:grid-cols-2 gap-4">
-                            <div>
-                                <h4 class="font-semibold text-gray-800 mb-2">Academic Databases:</h4>
-                                <ul class="text-sm text-gray-600 space-y-1">
-                                    <li>• PubMed/NCBI (~30+ million papers)</li>
-                                    <li>• arXiv (~2+ million preprints)</li>
-                                    <li>• NASA ADS (~15+ million papers)</li>
-                                    <li>• Zenodo (100K+ datasets)</li>
-                                    <li>• bioRxiv/medRxiv (preprints)</li>
-                                    <li>• CORE (~200+ million papers)</li>
-                                    <li>• Google Scholar (comprehensive)</li>
-                                    <li>• News API (current events)</li>
-                                    <li>• YouTube Data API (academic videos)</li>
-                                </ul>
-                            </div>
-                        </div>
-                    </div>
-                </div>
-            </div>
+    <!-- What is the Framework -->
+    <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">
+            <h2 class="text-3xl font-bold text-gray-900 mb-6">🎯 What is the Programming Framework?</h2>
+            <div class="prose max-w-none">
+                <p class="text-lg text-gray-700 mb-4">
+                    The Programming Framework is a <strong>meta-tool</strong>—a tool for creating tools. It provides a 
+                    systematic method for analyzing any complex process by combining the analytical power of Large Language 
+                    Models with the clarity of visual flowcharts.
+                </p>
 
-            <!-- Audio and Video Podcast Production -->
-            <div class="bg-white rounded-xl shadow-lg p-8">
-                <div class="flex items-start mb-4">
-                    <span class="text-4xl mr-4">🎙️</span>
-                    <div class="flex-1">
-                        <h3 class="text-2xl font-bold text-gray-900 mb-3">Audio and Video Podcast Production</h3>
-                        <p class="text-gray-600 mb-4">
-                            <strong>Operating Audio Podcast System:</strong> Full production and distribution platform for subscriber-generated 
-                            podcasts. Users can prompt, generate, publish, and distribute audio podcasts with RSS feed support for 
-                            Spotify, Apple Podcasts, and Google Podcasts.
+                <div class="grid md:grid-cols-2 gap-6 mt-6">
+                    <div class="bg-orange-50 rounded-lg p-6">
+                        <h3 class="text-xl font-semibold text-gray-900 mb-3">🔍 The Problem</h3>
+                        <p class="text-gray-700">
+                            Complex processes—whether biological, computational, or organizational—are difficult to 
+                            understand because they involve many steps, decision points, and interactions. Traditional 
+                            descriptions in text are hard to follow.
                         </p>
-                        <div class="bg-green-50 rounded-lg p-4 mb-4">
-                            <h4 class="font-semibold text-gray-800 mb-2">Current Audio Capabilities (Operational):</h4>
-                            <ul class="text-sm text-gray-700 space-y-1">
-                                <li>✓ Multi-voice AI podcast generation</li>
-                                <li>✓ Research-driven content creation</li>
-                                <li>✓ RSS feed distribution</li>
-                                <li>✓ Public and private podcast options</li>
-                                <li>✓ Professional audio quality</li>
-                            </ul>
-                        </div>
-                        <div class="bg-blue-50 rounded-lg p-4 mt-4">
-                            <h4 class="font-semibold text-gray-800 mb-2">Video Production (Future - Phase 2+):</h4>
-                            <p class="text-sm text-gray-700 mb-2">Advanced video features planned for future development:</p>
-                            <ul class="text-sm text-gray-700 space-y-2">
-                                <li>• <strong>Visual Content Integration:</strong> Automated extraction from papers, web scraping, JSON database integration</li>
-                                <li>• <strong>Dynamic Visualizations:</strong> Scientific animations, real-time charts, LaTeX rendering</li>
-                                <li>• <strong>External Video Quoting:</strong> YouTube segment extraction with attribution & fair use compliance</li>
-                                <li>• <strong>Advanced Composition:</strong> Multi-layer video, auto subtitles, text overlays, professional transitions</li>
-                            </ul>
-                            <p class="text-xs text-gray-600 mt-2">
-                                See: <a href="https://huggingface.co/spaces/garywelz/sciencevideodb" class="text-blue-600 hover:underline">Science Video Database</a> - Companion project for research video content management.
-                            </p>
-                        </div>
                     </div>
-                </div>
-            </div>
 
-            <!-- Research Papers Metadata Database -->
-            <div class="bg-white rounded-xl shadow-lg p-8">
-                <div class="flex items-start mb-4">
-                    <span class="text-4xl mr-4">📚</span>
-                    <div class="flex-1">
-                        <h3 class="text-2xl font-bold text-gray-900 mb-3">Research Papers Metadata Database (Phase 2)</h3>
-                        <p class="text-gray-600 mb-4">
-                            A centralized <strong>metadata repository</strong> (not a file archive) providing structured JSON objects 
-                            with AI-powered preprocessing.
+                    <div class="bg-blue-50 rounded-lg p-6">
+                        <h3 class="text-xl font-semibold text-gray-900 mb-3">✨ The Solution</h3>
+                        <p class="text-gray-700">
+                            Use LLMs to extract process logic from literature, then encode it as Mermaid flowcharts 
+                            stored in JSON. Result: Clear, interactive visualizations that reveal hidden patterns and 
+                            enable systematic analysis.
                         </p>
-                        <div class="grid md:grid-cols-2 gap-4">
-                            <div>
-                                <h4 class="font-semibold text-gray-800 mb-2">Structured JSON Objects:</h4>
-                                <ul class="text-sm text-gray-600 space-y-1">
-                                    <li>• DOI, arXiv ID, publication info</li>
-                                    <li>• Abstracts & key findings</li>
-                                    <li>• Extracted entities (genes, proteins, compounds, equations)</li>
-                                    <li>• Citation networks & cross-references</li>
-                                    <li>• Paradigm shift indicators</li>
-                                    <li>• Quality scores & relevance metrics</li>
-                                </ul>
-                            </div>
-                            <div>
-                                <h4 class="font-semibold text-gray-800 mb-2">AI-Powered Preprocessing:</h4>
-                                <ul class="text-sm text-gray-600 space-y-1">
-                                    <li>• LLM-based entity extraction</li>
-                                    <li>• Automatic categorization</li>
-                                    <li>• Keyword extraction & semantic tagging</li>
-                                    <li>• Citation tracking & mapping</li>
-                                    <li>• Quality assessment</li>
-                                    <li>• RESTful API access</li>
-                                </ul>
-                            </div>
-                        </div>
                     </div>
                 </div>
             </div>
         </div>
     </section>
 
-    <!-- Technology Stack -->
+    <!-- How It Works -->
     <section class="max-w-7xl mx-auto px-4 sm:px-6 lg:px-8 py-8">
-        <div class="bg-white rounded-xl shadow-lg p-8">
-            <h2 class="text-3xl font-bold text-gray-900 mb-6">⚙️ Technology Stack</h2>
+        <div class="bg-gradient-to-r from-orange-50 to-yellow-50 rounded-xl p-8">
+            <h2 class="text-3xl font-bold text-gray-900 mb-8 text-center">⚙️ How It Works</h2>
             
-            <div class="grid md:grid-cols-3 gap-6 mb-6">
-                <div>
-                    <h3 class="text-lg font-semibold text-gray-800 mb-3">AI & Machine Learning</h3>
-                    <ul class="text-sm text-gray-600 space-y-1">
-                        <li>• Google Gemini 3</li>
-                        <li>• Google Vertex AI (model orchestration)</li>
-                        <li>• OpenAI GPT-4/GPT-3.5</li>
-                        <li>• Anthropic Claude 3</li>
-                        <li>• ElevenLabs TTS</li>
-                        <li>• DALL-E 3</li>
-                        <li>• Cloud Vision API</li>
-                        <li>• Video Intelligence API</li>
-                    </ul>
+            <div class="grid md:grid-cols-4 gap-6">
+                <div class="bg-white rounded-lg p-6 text-center">
+                    <div class="text-4xl mb-3">1️⃣</div>
+                    <h3 class="font-semibold text-gray-900 mb-2">Input Process</h3>
+                    <p class="text-sm text-gray-600">Provide scientific papers, documentation, or process descriptions</p>
                 </div>
-                
-                <div>
-                    <h3 class="text-lg font-semibold text-gray-800 mb-3">Backend Infrastructure</h3>
-                    <ul class="text-sm text-gray-600 space-y-1">
-                        <li>• FastAPI (Python)</li>
-                        <li>• Google Cloud Run</li>
-                        <li>• Firestore (NoSQL)</li>
-                        <li>• Cloud Storage</li>
-                        <li>• Cloud Functions</li>
-                        <li>• Cloud Tasks</li>
-                        <li>• Secret Manager</li>
-                    </ul>
+
+                <div class="bg-white rounded-lg p-6 text-center">
+                    <div class="text-4xl mb-3">2️⃣</div>
+                    <h3 class="font-semibold text-gray-900 mb-2">LLM Analysis</h3>
+                    <p class="text-sm text-gray-600">AI extracts steps, decisions, branches, and logic flow</p>
                 </div>
-                
-                <div>
-                    <h3 class="text-lg font-semibold text-gray-800 mb-3">Frontend</h3>
-                    <ul class="text-sm text-gray-600 space-y-1">
-                        <li>• Next.js 15.5.7</li>
-                        <li>• Alpine.js</li>
-                        <li>• Tailwind CSS</li>
-                        <li>• Vercel</li>
-                    </ul>
+
+                <div class="bg-white rounded-lg p-6 text-center">
+                    <div class="text-4xl mb-3">3️⃣</div>
+                    <h3 class="font-semibold text-gray-900 mb-2">Generate Flowchart</h3>
+                    <p class="text-sm text-gray-600">Create Mermaid diagram encoded as JSON structure</p>
                 </div>
-            </div>
-        </div>
-    </section>
 
-    <!-- Research & Collaborative Tools -->
-    <section class="max-w-7xl mx-auto px-4 sm:px-6 lg:px-8 py-8">
-        <div class="bg-gradient-to-r from-green-50 to-blue-50 rounded-xl p-8">
-            <h2 class="text-3xl font-bold text-gray-900 mb-6">🔬 Collaborative Research Tools</h2>
-            
-            <div class="grid md:grid-cols-2 gap-6 mb-6">
-                <div>
-                    <h3 class="text-xl font-semibold text-gray-800 mb-3">Collaborative Research Tools</h3>
-                    <p class="text-gray-700 mb-3">
-                        These platforms enable collective participation and collaboration across diverse user communities:
-                    </p>
-                    <ul class="text-gray-700 space-y-2">
-                        <li>• <strong>Researchers</strong> - Tools for hypothesis formation and testing, cross-disciplinary synthesis</li>
-                        <li>• <strong>Collaborators</strong> - Collective knowledge exploration and refinement</li>
-                        <li>• <strong>Subscribers</strong> - Prompt, generate, and share podcasts (public or private)</li>
-                        <li>• <strong>Community</strong> - User suggestions, comments, and collaborative flowchart improvement (GLMP)</li>
-                    </ul>
-                    <p class="text-gray-600 mt-4 italic">
-                        Like a microscope enables observation of the microscopic world, these tools enable observation and 
-                        exploration of humanity's collective knowledge.
-                    </p>
+                <div class="bg-white rounded-lg p-6 text-center">
+                    <div class="text-4xl mb-3">4️⃣</div>
+                    <h3 class="font-semibold text-gray-900 mb-2">Visualize & Iterate</h3>
+                    <p class="text-sm text-gray-600">Interactive flowchart reveals insights and enables refinement</p>
                 </div>
-                
-                <div>
-                    <h3 class="text-xl font-semibold text-gray-800 mb-3">Key Innovations</h3>
-                    <ul class="text-gray-700 space-y-2">
-                        <li>• Multi-source validation (min 3 sources)</li>
-                        <li>• Evidence-based generation</li>
-                        <li>• Paradigm shift detection</li>
-                        <li>• Interdisciplinary connections</li>
-                        <li>• Multiple expertise levels</li>
-                        <li>• Full citation tracking</li>
-                    </ul>
+            </div>
+
+            <div class="mt-8 bg-white rounded-lg p-6">
+                <h4 class="font-semibold text-gray-900 mb-3">📊 Live Example:</h4>
+                <div id="exampleDiagram" class="mermaid">
+                    graph TD
+                        A[Complex Process Input] --> B{LLM Analysis}
+                        B -->|Extract Logic| C[Identify Steps]
+                        B -->|Extract Decisions| D[Identify Branches]
+                        C --> E[Create Flowchart Nodes]
+                        D --> F[Create Decision Points]
+                        E --> G[Generate Mermaid Syntax]
+                        F --> G
+                        G --> H[Store as JSON]
+                        H --> I[Interactive Visualization]
+                        I --> J{Insights Gained?}
+                        J -->|No| K[Refine Analysis]
+                        J -->|Yes| L[Apply Knowledge]
+                        K --> B
                 </div>
             </div>
         </div>
     </section>
 
-    <!-- Prior Work & Research Contributions -->
+    <!-- Core Principles -->
     <section class="max-w-7xl mx-auto px-4 sm:px-6 lg:px-8 py-8">
-        <div class="bg-gradient-to-r from-purple-50 to-blue-50 rounded-xl shadow-lg p-8">
-            <h2 class="text-3xl font-bold text-gray-900 mb-6">📚 Prior Work & Research Contributions</h2>
-            
-            <div class="bg-white rounded-lg p-6 mb-6">
-                <h3 class="text-xl font-semibold text-gray-900 mb-4">Overview</h3>
-                <p class="text-gray-700 mb-4">
-                    This platform represents <strong>prior work</strong> that demonstrates foundational research and development 
-                    achievements in AI-powered scientific knowledge synthesis, collaborative research tools, and multi-modal content 
-                    generation. These contributions establish the technical foundation and proof-of-concept for the broader 
-                    <strong>CopernicusAI Knowledge Engine</strong> initiative.
+        <h2 class="text-3xl font-bold text-gray-900 mb-6">💡 Core Principles</h2>
+        
+        <div class="grid md:grid-cols-3 gap-6">
+            <div class="bg-white rounded-lg shadow-md p-6 card-hover">
+                <div class="text-4xl mb-3">🌍</div>
+                <h3 class="text-xl font-semibold text-gray-900 mb-3">Domain Agnostic</h3>
+                <p class="text-gray-600">
+                    Works across any field: biology, chemistry, software engineering, business processes, 
+                    legal workflows, manufacturing, and beyond.
                 </p>
             </div>
 
-            <div class="grid md:grid-cols-2 gap-6 mb-6">
-                <div class="bg-white rounded-lg p-6">
-                    <h3 class="text-lg font-semibold text-gray-900 mb-3">🔬 Research Contributions</h3>
-                    <ul class="text-sm text-gray-700 space-y-2">
-                        <li>• <strong>AI-Powered Research Synthesis:</strong> Production system for multi-source research synthesis using LLMs</li>
-                        <li>• <strong>Multi-Model Architecture:</strong> Intelligent model selection with Gemini 3, GPT-4, Claude 3</li>
-                        <li>• <strong>Collaborative Platform:</strong> Subscriber-driven content generation with public/private sharing</li>
-                        <li>• <strong>Knowledge Engine Integration:</strong> Architecture for Research Papers DB, Video DB, GLMP, Framework</li>
-                    </ul>
-                </div>
-                
-                <div class="bg-white rounded-lg p-6">
-                    <h3 class="text-lg font-semibold text-gray-900 mb-3">⚙️ Technical Achievements</h3>
-                    <ul class="text-sm text-gray-700 space-y-2">
-                        <li>• <strong>250+ Million Papers:</strong> Accessible via 8+ integrated academic databases</li>
-                        <li>• <strong>64+ Episodes:</strong> Generated across 5 scientific disciplines</li>
-                        <li>• <strong>Production Deployment:</strong> Live platform with operational API and RSS distribution</li>
-                        <li>• <strong>Scalable Architecture:</strong> Serverless microservices on Google Cloud</li>
-                    </ul>
-                </div>
-            </div>
-
-            <div class="bg-white rounded-lg p-6 mb-6">
-                <h3 class="text-lg font-semibold text-gray-900 mb-3">🎯 Position Within CopernicusAI Knowledge Engine</h3>
-                <p class="text-gray-700 mb-3">
-                    This platform serves as the <strong>core synthesis and distribution component</strong> of the CopernicusAI Knowledge Engine. 
-                    The Knowledge Engine is an integrated ecosystem of research and collaboration tools that work together to assist scientists 
-                    in their workflow, from research discovery through knowledge synthesis to multi-format content generation.
+            <div class="bg-white rounded-lg shadow-md p-6 card-hover">
+                <div class="text-4xl mb-3">🔄</div>
+                <h3 class="text-xl font-semibold text-gray-900 mb-3">Iterative Refinement</h3>
+                <p class="text-gray-600">
+                    Start with rough analysis, visualize, identify gaps, refine with LLM, repeat until 
+                    the process logic is crystal clear.
                 </p>
-                <div class="bg-blue-50 rounded-lg p-4 mb-3">
-                    <h4 class="font-semibold text-gray-900 mb-2">Current Components:</h4>
-                    <div class="grid md:grid-cols-2 gap-4 text-sm">
-                        <ul class="text-gray-700 space-y-1">
-                            <li>1. <strong>Copernicus AI</strong> (This platform) - Core synthesis & distribution</li>
-                            <li>2. <strong>Programming Framework</strong> - Foundational meta-tool</li>
-                            <li>3. <strong>GLMP</strong> - Biological process visualization</li>
-                        </ul>
-                        <ul class="text-gray-700 space-y-1">
-                            <li>4. <strong>Research Paper Metadata Database</strong> - Data infrastructure</li>
-                            <li>5. <strong>Science Video Database</strong> - Multi-modal content</li>
-                        </ul>
-                    </div>
-                </div>
-                <div class="bg-purple-50 rounded-lg p-4">
-                    <h4 class="font-semibold text-gray-900 mb-2">Future Development:</h4>
-                    <p class="text-gray-700 text-sm">
-                        The Knowledge Engine is designed to grow and evolve. Additional tools, databases, and collaboration components 
-                        will be added as the project develops, expanding capabilities for AI-assisted scientific research and knowledge discovery.
-                    </p>
-                </div>
             </div>
 
-            <div class="bg-blue-50 rounded-lg p-6">
-                <h3 class="text-lg font-semibold text-gray-900 mb-3">📖 Citation Information</h3>
-                <p class="text-sm text-gray-700 mb-3">
-                    <strong>For Grant Proposals (NSF/DOE):</strong>
+            <div class="bg-white rounded-lg shadow-md p-6 card-hover">
+                <div class="text-4xl mb-3">📦</div>
+                <h3 class="text-xl font-semibold text-gray-900 mb-3">Structured Data</h3>
+                <p class="text-gray-600">
+                    JSON storage enables programmatic access, version control, cross-referencing, 
+                    and integration with other tools and databases.
                 </p>
-                <div class="bg-white rounded p-4 font-mono text-sm text-gray-800">
-                    <p class="mb-2">Welz, G. (2025). Copernicus AI: Knowledge Engine for Scientific Discovery.</p>
-                    <p class="mb-2">Hugging Face Space. https://huggingface.co/spaces/garywelz/copernicusai</p>
-                    <p>Live Platform: https://www.copernicusai.fyi</p>
-                </div>
             </div>
         </div>
     </section>
 
-    <!-- How to Cite This Work -->
+    <!-- Applications -->
     <section class="max-w-7xl mx-auto px-4 sm:px-6 lg:px-8 py-8">
         <div class="bg-white rounded-xl shadow-lg p-8">
-            <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">
-                <p class="text-gray-800 font-mono text-lg leading-relaxed">
-                    Welz, G. (2024–2025). <em>CopernicusAI: AI-Generated Audio Briefings as a Research Interface</em>.<br>
-                    Hugging Face Spaces. https://huggingface.co/spaces/garywelz/copernicusai
-                </p>
+            <h2 class="text-3xl font-bold text-gray-900 mb-6">🚀 Applications</h2>
+            
+            <div class="grid md:grid-cols-2 gap-6">
+                <div class="border-l-4 border-green-500 pl-4 py-3">
+                    <h3 class="font-semibold text-gray-900 mb-2">🧬 GLMP - Genome Logic Modeling</h3>
+                    <p class="text-gray-600 mb-2">
+                        First specialized application: visualizing biochemical processes like DNA replication, 
+                        metabolic pathways, and cell signaling.
+                    </p>
+                    <a href="https://huggingface.co/spaces/garywelz/glmp" class="text-green-600 hover:text-green-700 text-sm font-semibold">
+                        Explore GLMP →
+                    </a>
+                </div>
+
+                <div class="border-l-4 border-blue-500 pl-4 py-3">
+                    <h3 class="font-semibold text-gray-900 mb-2">🧬 Biology Processes</h3>
+                    <p class="text-gray-600 mb-2">
+                        Comprehensive collection of biological process visualizations using the Programming Framework.
+                    </p>
+                    <a href="https://huggingface.co/spaces/garywelz/programming_framework/blob/main/biology_processes.html" 
+                       class="text-blue-600 hover:text-blue-700 text-sm font-semibold"
+                       target="_blank" rel="noopener noreferrer">
+                        View Biology Processes →
+                    </a>
+                </div>
+
+                <div class="border-l-4 border-purple-500 pl-4 py-3">
+                    <h3 class="font-semibold text-gray-900 mb-2">⚗️ Chemistry Processes</h3>
+                    <p class="text-gray-600 mb-2">
+                        Extensive collection of chemistry process diagrams across all major branches of chemistry.
+                    </p>
+                    <a href="https://huggingface.co/spaces/garywelz/programming_framework/blob/main/chemistry_index.html" 
+                       class="text-purple-600 hover:text-purple-700 text-sm font-semibold"
+                       target="_blank" rel="noopener noreferrer">
+                        View Chemistry Processes →
+                    </a>
+                </div>
+
+                <div class="border-l-4 border-orange-500 pl-4 py-3">
+                    <h3 class="font-semibold text-gray-900 mb-2">🔢 Mathematics Processes</h3>
+                    <p class="text-gray-600 mb-2">
+                        Mathematical algorithms, proof methods, and computational processes visualized as flowcharts.
+                    </p>
+                    <a href="https://huggingface.co/spaces/garywelz/programming_framework/blob/main/mathematics_processes.html" 
+                       class="text-orange-600 hover:text-orange-700 text-sm font-semibold"
+                       target="_blank" rel="noopener noreferrer">
+                        View Mathematics Processes →
+                    </a>
+                </div>
+
+                <div class="border-l-4 border-indigo-500 pl-4 py-3">
+                    <h3 class="font-semibold text-gray-900 mb-2">⚛️ Physics Processes</h3>
+                    <p class="text-gray-600 mb-2">
+                        Physical processes including quantum mechanics, thermodynamics, and particle physics.
+                    </p>
+                    <a href="https://huggingface.co/spaces/garywelz/programming_framework/blob/main/physics_processes.html" 
+                       class="text-indigo-600 hover:text-indigo-700 text-sm font-semibold"
+                       target="_blank" rel="noopener noreferrer">
+                        View Physics Processes →
+                    </a>
+                </div>
+
+                <div class="border-l-4 border-teal-500 pl-4 py-3">
+                    <h3 class="font-semibold text-gray-900 mb-2">💻 Computer Science Processes</h3>
+                    <p class="text-gray-600 mb-2">
+                        Algorithms, software engineering workflows, and computational processes.
+                    </p>
+                    <a href="https://huggingface.co/spaces/garywelz/programming_framework/blob/main/computer_science_index.html" 
+                       class="text-teal-600 hover:text-teal-700 text-sm font-semibold"
+                       target="_blank" rel="noopener noreferrer">
+                        View Computer Science Processes →
+                    </a>
+                </div>
             </div>
         </div>
     </section>
-        </div>
-    </section>
 
-    <!-- Grant Support & Collaboration -->
+    <!-- Process Diagram Collections -->
     <section class="max-w-7xl mx-auto px-4 sm:px-6 lg:px-8 py-8">
-        <div class="bg-white rounded-xl shadow-lg p-8">
-            <h2 class="text-3xl font-bold text-gray-900 mb-6">🌐 Grant Support & Collaboration</h2>
+        <div class="bg-gradient-to-r from-green-50 to-blue-50 rounded-xl shadow-lg p-8">
+            <h2 class="text-3xl font-bold text-gray-900 mb-6">📚 Process Diagram Collections</h2>
+            <p class="text-gray-700 mb-6">
+                The Programming Framework has been applied across multiple scientific disciplines. Explore interactive flowchart collections organized by domain:
+            </p>
             
-            <div class="mb-6">
-                <h3 class="text-xl font-semibold text-gray-800 mb-3">Grant Applications Supported</h3>
-                <p class="text-gray-700 mb-4">
-                    This platform is designed to support grant applications to:
-                </p>
-                <div class="grid md:grid-cols-3 gap-4">
-                    <div class="bg-blue-50 rounded-lg p-4">
-                        <h4 class="font-semibold text-gray-800 mb-2">NSF</h4>
-                        <p class="text-sm text-gray-600">National Science Foundation - Science education and research infrastructure</p>
-                    </div>
-                    <div class="bg-green-50 rounded-lg p-4">
-                        <h4 class="font-semibold text-gray-800 mb-2">DOE</h4>
-                        <p class="text-sm text-gray-600">Department of Energy - Scientific computing and data science</p>
-                    </div>
-                    <div class="bg-purple-50 rounded-lg p-4">
-                        <h4 class="font-semibold text-gray-800 mb-2">SAIR Foundation</h4>
-                        <p class="text-sm text-gray-600">AI research and development initiatives</p>
-                    </div>
+            <div class="grid md:grid-cols-2 lg:grid-cols-3 gap-6">
+                <!-- Biology -->
+                <div class="bg-white rounded-lg shadow-md p-6 card-hover">
+                    <h3 class="text-xl font-semibold text-gray-900 mb-4 flex items-center">
+                        <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).
+                    </p>
+                    <a href="https://huggingface.co/spaces/garywelz/programming_framework/blob/main/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>
-            </div>
-            
-            <div>
-                <h3 class="text-xl font-semibold text-gray-800 mb-3">Collaboration Opportunities</h3>
-                <ul class="text-gray-700 space-y-2">
-                    <li>• Integration with academic institutions</li>
-                    <li>• Partnership with research organizations</li>
-                    <li>• Open data initiatives</li>
-                    <li>• Educational program development</li>
-                </ul>
-            </div>
-        </div>
-    </section>
 
-    <!-- Links & Resources -->
-    <section class="max-w-7xl mx-auto px-4 sm:px-6 lg:px-8 py-12">
-        <div class="bg-gradient-to-r from-blue-50 to-purple-50 rounded-xl p-8">
-            <h2 class="text-3xl font-bold text-gray-900 mb-6 text-center">🔗 Live Platform & Resources</h2>
-            
-            <div class="grid md:grid-cols-2 gap-6">
-                <div class="bg-white rounded-lg p-6">
-                    <h3 class="text-xl font-semibold text-gray-800 mb-4">🌐 Production Deployment</h3>
-                    <ul class="space-y-2">
-                        <li>
-                            <a href="https://www.copernicusai.fyi" target="_blank" 
-                               class="text-blue-600 hover:text-blue-800 font-medium">
-                                🏠 Homepage - Browse Podcasts
-                            </a>
-                        </li>
-                        <li>
-                            <a href="https://www.copernicusai.fyi/subscriber-dashboard.html" target="_blank" 
-                               class="text-blue-600 hover:text-blue-800 font-medium">
-                                📊 Creator Dashboard
-                            </a>
-                        </li>
-                        <li>
-                            <a href="https://storage.googleapis.com/regal-scholar-453620-r7-podcast-storage/feeds/copernicus-mvp-rss-feed.xml" target="_blank" 
-                               class="text-blue-600 hover:text-blue-800 font-medium">
-                                📡 RSS Feed
-                            </a>
-                        </li>
-                    </ul>
+                <!-- Chemistry -->
+                <div class="bg-white rounded-lg shadow-md p-6 card-hover">
+                    <h3 class="text-xl font-semibold text-gray-900 mb-4 flex items-center">
+                        <span class="text-2xl mr-2">⚗️</span> Chemistry
+                    </h3>
+                    <p class="text-gray-600 text-sm mb-3">
+                        Comprehensive chemistry process diagrams across all major branches.
+                    </p>
+                    <a href="https://huggingface.co/spaces/garywelz/programming_framework/blob/main/chemistry_index.html" 
+                       class="text-orange-600 hover:text-orange-700 font-medium text-sm inline-block"
+                       target="_blank" rel="noopener noreferrer">
+                        Chemistry Index →
+                    </a>
                 </div>
-                
-                <div class="bg-white rounded-lg p-6">
-                    <h3 class="text-xl font-semibold text-gray-800 mb-4">🧩 Knowledge Engine Components</h3>
-                    <p class="text-sm text-gray-600 mb-4">
-                        The CopernicusAI Knowledge Engine is an integrated ecosystem of research and collaboration tools. 
-                        Additional components will be added as the project develops.
+
+                <!-- Mathematics -->
+                <div class="bg-white rounded-lg shadow-md p-6 card-hover">
+                    <h3 class="text-xl font-semibold text-gray-900 mb-4 flex items-center">
+                        <span class="text-2xl mr-2">🔢</span> Mathematics
+                    </h3>
+                    <p class="text-gray-600 text-sm mb-3">
+                        Mathematical algorithms, proof methods, and computational processes.
                     </p>
-                    <ul class="space-y-3">
-                        <li>
-                            <a href="https://huggingface.co/spaces/garywelz/programming_framework" target="_blank" 
-                               class="text-blue-600 hover:text-blue-800 font-medium">
-                                🛠️ Programming Framework
-                            </a>
-                            <p class="text-sm text-gray-600 mt-1 ml-6">
-                                Foundational meta-tool for universal process analysis across any discipline
-                            </p>
-                        </li>
-                        <li>
-                            <a href="https://huggingface.co/spaces/garywelz/glmp" target="_blank" 
-                               class="text-blue-600 hover:text-blue-800 font-medium">
-                                🧬 GLMP - Genome Logic Modeling Project
-                            </a>
-                            <p class="text-sm text-gray-600 mt-1 ml-6">
-                                First application of Programming Framework to biology - 50+ biological processes visualized
-                            </p>
-                        </li>
-                        <li>
-                            <a href="https://huggingface.co/spaces/garywelz/metadata_database" target="_blank" 
-                               class="text-blue-600 hover:text-blue-800 font-medium">
-                                📚 Research Paper Metadata Database
-                            </a>
-                            <p class="text-sm text-gray-600 mt-1 ml-6">
-                                Core data infrastructure for structured research paper metadata and citation networks
-                            </p>
-                        </li>
-                        <li>
-                            <a href="https://huggingface.co/spaces/garywelz/sciencevideodb" target="_blank" 
-                               class="text-blue-600 hover:text-blue-800 font-medium">
-                                🎬 Science Video Database
-                            </a>
-                            <p class="text-sm text-gray-600 mt-1 ml-6">
-                                Multi-modal content component with transcript-based search for scientific videos
-                            </p>
-                        </li>
-                    </ul>
+                    <a href="https://huggingface.co/spaces/garywelz/programming_framework/blob/main/mathematics_processes.html" 
+                       class="text-orange-600 hover:text-orange-700 font-medium text-sm inline-block"
+                       target="_blank" rel="noopener noreferrer">
+                        Mathematics Processes →
+                    </a>
+                </div>
+
+                <!-- Physics -->
+                <div class="bg-white rounded-lg shadow-md p-6 card-hover">
+                    <h3 class="text-xl font-semibold text-gray-900 mb-4 flex items-center">
+                        <span class="text-2xl mr-2">⚛️</span> Physics
+                    </h3>
+                    <p class="text-gray-600 text-sm mb-3">
+                        Physical processes including quantum mechanics, thermodynamics, and particle physics.
+                    </p>
+                    <a href="https://huggingface.co/spaces/garywelz/programming_framework/blob/main/physics_processes.html" 
+                       class="text-orange-600 hover:text-orange-700 font-medium text-sm inline-block"
+                       target="_blank" rel="noopener noreferrer">
+                        Physics Processes →
+                    </a>
+                </div>
+
+                <!-- Computer Science -->
+                <div class="bg-white rounded-lg shadow-md p-6 card-hover">
+                    <h3 class="text-xl font-semibold text-gray-900 mb-4 flex items-center">
+                        <span class="text-2xl mr-2">💻</span> Computer Science
+                    </h3>
+                    <p class="text-gray-600 text-sm mb-3">
+                        Algorithms, software engineering workflows, and computational processes.
+                    </p>
+                    <a href="https://huggingface.co/spaces/garywelz/programming_framework/blob/main/computer_science_index.html" 
+                       class="text-orange-600 hover:text-orange-700 font-medium text-sm inline-block"
+                       target="_blank" rel="noopener noreferrer">
+                        Computer Science Index →
+                    </a>
                 </div>
             </div>
         </div>
     </section>
 
-    <!-- API Endpoints -->
+    <!-- Technical Details -->
     <section class="max-w-7xl mx-auto px-4 sm:px-6 lg:px-8 py-8">
         <div class="bg-gray-900 text-white rounded-xl p-8">
-            <h2 class="text-3xl font-bold mb-6">🔌 API Documentation</h2>
-            <p class="text-gray-300 mb-6">Base URL: <code class="bg-gray-800 px-2 py-1 rounded">https://copernicus-podcast-api-phzp4ie2sq-uc.a.run.app</code></p>
+            <h2 class="text-3xl font-bold mb-6">⚙️ Technical Architecture</h2>
             
-            <div class="grid md:grid-cols-3 gap-4 text-sm">
+            <div class="grid md:grid-cols-2 gap-8">
                 <div>
-                    <h4 class="font-semibold text-blue-300 mb-2">Podcast Generation</h4>
-                    <ul class="space-y-1 text-gray-400">
-                        <li>POST /generate-podcast-with-subscriber</li>
-                        <li>GET /api/subscribers/podcasts/{id}</li>
-                        <li>POST /api/subscribers/podcasts/submit-to-rss</li>
+                    <h3 class="text-xl font-semibold text-orange-400 mb-4">🤖 LLM Integration</h3>
+                    <ul class="space-y-2 text-gray-300">
+                        <li>• Google Gemini 2.0 Flash for analysis</li>
+                        <li>• Vertex AI for enterprise deployment</li>
+                        <li>• Custom prompts for process extraction</li>
+                        <li>• Structured JSON output formatting</li>
                     </ul>
                 </div>
-                
+
                 <div>
-                    <h4 class="font-semibold text-blue-300 mb-2">Research Endpoints</h4>
-                    <ul class="space-y-1 text-gray-400">
-                        <li>POST /api/papers/upload</li>
-                        <li>GET /api/papers/{paper_id}</li>
-                        <li>POST /api/papers/query</li>
-                        <li>POST /api/papers/{id}/link-podcast/{id}</li>
+                    <h3 class="text-xl font-semibold text-orange-400 mb-4">📊 Visualization Stack</h3>
+                    <ul class="space-y-2 text-gray-300">
+                        <li>• Mermaid.js for flowchart rendering</li>
+                        <li>• JSON schema for data validation</li>
+                        <li>• Interactive SVG output</li>
+                        <li>• Export to PNG/PDF supported</li>
                     </ul>
                 </div>
-                
+
                 <div>
-                    <h4 class="font-semibold text-blue-300 mb-2">Admin Endpoints</h4>
-                    <ul class="space-y-1 text-gray-400">
-                        <li>GET /api/admin/subscribers</li>
-                        <li>POST /api/admin/podcasts/fix-missing-titles</li>
-                        <li>GET /api/admin/podcasts/catalog</li>
+                    <h3 class="text-xl font-semibold text-orange-400 mb-4">💾 Data Storage</h3>
+                    <ul class="space-y-2 text-gray-300">
+                        <li>• Google Cloud Storage for JSON files</li>
+                        <li>• Firestore for metadata indexing</li>
+                        <li>• Version control with Git</li>
+                        <li>• Cross-referencing with papers database</li>
+                    </ul>
+                </div>
+
+                <div>
+                    <h3 class="text-xl font-semibold text-orange-400 mb-4">🔗 Integration Points</h3>
+                    <ul class="space-y-2 text-gray-300">
+                        <li>• GLMP specialized collections</li>
+                        <li>• Copernicus AI knowledge graph</li>
+                        <li>• Research papers database</li>
+                        <li>• API endpoints for programmatic access</li>
                     </ul>
                 </div>
             </div>
         </div>
     </section>
 
+    <!-- Related Projects -->
+    <section class="max-w-7xl mx-auto px-4 sm:px-6 lg:px-8 py-8">
+        <h2 class="text-3xl font-bold text-gray-900 mb-6 text-center">🔗 Related Projects</h2>
+        
+        <div class="grid md:grid-cols-2 gap-6">
+            <div class="bg-white rounded-lg shadow-md p-6 card-hover">
+                <h3 class="text-xl font-semibold text-gray-900 mb-3">🧬 GLMP - Genome Logic Modeling</h3>
+                <p class="text-gray-600 mb-4">
+                    First specialized application of the Programming Framework to biochemical processes.
+                    50+ biological pathways visualized as interactive flowcharts.
+                </p>
+                <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 →
+                </a>
+            </div>
+
+            <div class="bg-white rounded-lg shadow-md p-6 card-hover">
+                <h3 class="text-xl font-semibold text-gray-900 mb-3">🔬 Copernicus AI</h3>
+                <p class="text-gray-600 mb-4">
+                    Knowledge engine integrating the Programming Framework with AI podcasts, research papers,
+                    and knowledge graph for scientific discovery.
+                </p>
+                <a href="https://www.copernicusai.fyi" 
+                   class="text-orange-600 hover:text-orange-700 font-semibold"
+                   target="_blank" rel="noopener noreferrer">
+                    Visit Copernicus AI →
+                </a>
+            </div>
+        </div>
+    </section>
+
+    <!-- How to Cite This Work -->
+    <section class="max-w-7xl mx-auto px-4 sm:px-6 lg:px-8 py-8">
+        <div class="bg-white rounded-xl shadow-lg p-8">
+            <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">
+                        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>
+                    </p>
+                </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>
+                    </p>
+                </div>
+            </div>
+            <div class="bg-orange-50 rounded-lg p-4">
+                <p class="text-gray-700 mb-2">
+                    This project serves as a foundational meta-tool for AI-assisted process analysis, enabling systematic extraction and visualization of complex logic from textual sources across diverse scientific and technical domains.
+                </p>
+                <p class="text-gray-700 font-semibold">
+                    The Programming Framework is designed as infrastructure for AI-assisted science, providing a universal methodology that can be specialized for domain-specific applications.
+                </p>
+            </div>
+        </div>
+    </section>
+
     <!-- Footer -->
     <footer class="gradient-bg text-white py-8 mt-12">
         <div class="max-w-7xl mx-auto px-4 sm:px-6 lg:px-8 text-center">
-            <p class="text-lg font-semibold mb-2">Copernicus AI - Advancing Scientific Knowledge</p>
-            <p class="text-sm opacity-75">Built with Google Cloud, Gemini AI, OpenAI, Anthropic Claude, and ElevenLabs</p>
-            <p class="text-xs opacity-50 mt-4">&copy; 2025 Copernicus AI. All rights reserved.</p>
+            <p class="text-lg font-semibold mb-2">The Programming Framework</p>
+            <p class="text-sm opacity-75">A Universal Method for Process Analysis</p>
+            <p class="text-xs opacity-50 mt-4">&copy; 2025 Gary Welz. All rights reserved.</p>
         </div>
     </footer>
+
+    <script>
+        mermaid.initialize({ startOnLoad: true, theme: 'default' });
+    </script>
 </body>
 </html>
+

physics_processes.html

@@ -1,653 +1,158 @@
 <!DOCTYPE html>
 <html lang="en">
 <head>
-    <meta charset="UTF-8" />
-    <meta name="viewport" content="width=device-width, initial-scale=1" />
-    <title>Physics Processes - Programming Framework Analysis</title>
+    <meta charset="UTF-8">
+    <meta name="viewport" content="width=device-width, initial-scale=1.0">
+    <title>Physics Processes - Programming Framework</title>
     <style>
-        body { 
-            font-family: 'Times New Roman', Times, serif, 'Arial Unicode MS'; 
-            margin: 0; 
-            background: #ffffff; 
-            color: #000000; 
-            line-height: 1.6; 
-            font-size: 12pt; 
+        body {
+            font-family: 'Times New Roman', Times, serif, 'Arial Unicode MS';
+            margin: 0;
+            background: #ffffff;
+            color: #000000;
+            line-height: 1.6;
+            font-size: 12pt;
         }
-        .container { 
-            max-width: 1000px; 
-            margin: 0 auto; 
-            padding: 1.5rem; 
+        .container {
+            max-width: 1000px;
+            margin: 0 auto;
+            padding: 1.5rem;
         }
-        h1, h2, h3 { 
-            color: #000000; 
-            margin-top: 1.5rem; 
-            margin-bottom: 0.75rem; 
+        h1, h2, h3 {
+            color: #000000;
+            margin-top: 1.5rem;
+            margin-bottom: 0.75rem;
         }
-        h1 { 
-            font-size: 18pt; 
-            text-align: center; 
+        h1 {
+            font-size: 18pt;
+            text-align: center;
         }
-        h2 { 
-            font-size: 16pt; 
-            border-bottom: 2px solid #000; 
-            padding-bottom: 0.5rem; 
+        h2 {
+            font-size: 16pt;
+            border-bottom: 2px solid #000;
+            padding-bottom: 0.5rem;
         }
-        h3 { 
-            font-size: 14pt; 
+        h3 {
+            font-size: 14pt;
         }
-        p { 
-            margin-bottom: 1rem; 
-            text-align: justify; 
+        .batch-links {
+            margin: 1rem 0;
         }
-        .figure { 
-            margin: 1rem 0; 
-            text-align: center; 
-            border: 1px solid #ccc; 
-            padding: 1rem; 
-            background: #f9f9f9; 
+        .batch-link {
+            display: block;
+            padding: 1rem;
+            margin: 0.5rem 0;
+            background: #f8f9fa;
+            border-left: 4px solid #007bff;
+            text-decoration: none;
+            color: #000;
+            transition: background 0.3s;
         }
-        .figure-caption { 
-            margin-top: 1rem; 
-            font-style: italic; 
-            text-align: left; 
+        .batch-link:hover {
+            background: #e9ecef;
         }
-        .mermaid { 
-            background: white; 
-            padding: 1rem; 
-            border-radius: 4px; 
+        .batch-number {
+            font-weight: bold;
+            color: #007bff;
+            display: block;
+            margin-bottom: 0.25rem;
+        }
+        .batch-title {
+            display: block;
+            font-size: 11pt;
+            color: #333;
+        }
+        .navigation {
+            margin: 2rem 0;
+            padding: 1.5rem;
+            background: #f8f9fa;
+            border-radius: 8px;
+        }
+        .nav-links {
+            display: flex;
+            flex-wrap: wrap;
+            gap: 1rem;
+        }
+        .nav-link {
+            padding: 0.5rem 1rem;
+            background: #007bff;
+            color: white;
+            text-decoration: none;
+            border-radius: 4px;
+            font-size: 11pt;
+        }
+        .nav-link:hover {
+            background: #0056b3;
+        }
+        .footer {
+            margin-top: 3rem;
+            padding-top: 2rem;
+            border-top: 2px solid #000;
+            text-align: center;
+            font-size: 10pt;
+        }
+        .contact-info {
+            margin-top: 1rem;
         }
     </style>
-    <script src="https://cdn.jsdelivr.net/npm/mermaid@10.6.1/dist/mermaid.min.js"></script>
-    <script>
-        mermaid.initialize({ 
-            startOnLoad: true, 
-            theme: 'default', 
-            flowchart: { 
-                useMaxWidth: false, 
-                htmlLabels: true,
-                curve: 'linear',
-                nodeSpacing: 50,
-                rankSpacing: 50,
-                padding: 20
-            },
-            themeVariables: {
-                fontFamily: 'Arial Unicode MS, Arial, sans-serif'
-            }
-        });
-    </script>
 </head>
 <body>
     <div class="container">
-        <h1>Physics Processes - Programming Framework Analysis</h1>
-        
-        <p>This document presents physics 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>
+        <h1>⚛️ Physics Processes</h1>
+        <p class="subtitle" style="text-align: center; font-style: italic; color: #666; margin-bottom: 2rem;">
+            Programming Framework Process Visualizations
+        </p>
 
-        <h2>1. Quantum Tunneling Process</h2>
-        <div class="figure">
-            <div class="mermaid">
-graph TD
-    %% Initial Conditions
-    A1[Particle Energy E] --> B1[Energy Assessment]
-    C1[Barrier Height V0] --> D1[Barrier Analysis]
-    E1[Barrier Width a] --> F1[Geometric Constraints]
-    
-    %% Quantum State Preparation
-    B1 --> G1[Wave Function Initialization]
-    D1 --> H1[Potential Energy Profile]
-    F1 --> I1[Spatial Boundary Conditions]
-    
-    %% Wave Function Evolution
-    G1 --> J1[Incident Wave Function psi1]
-    H1 --> K1[Barrier Region psi2]
-    I1 --> L1[Transmitted Wave Function psi3]
-    
-    %% Quantum Processing
-    J1 --> M1[Wave Function Matching]
-    K1 --> N1[Exponential Decay in Barrier]
-    L1 --> O1[Transmission Coefficient Calculation]
-    
-    %% Quantum State Analysis
-    M1 --> P1[Boundary Condition Equations]
-    N1 --> Q1[Quantum Amplitude Processing]
-    O1 --> R1[Probability Density Analysis]
-    
-    %% Transmission Calculation
-    P1 --> S1[Wave Function Continuity]
-    Q1 --> T1[Quantum Interference Effects]
-    R1 --> U1[Transmission Probability T]
-    
-    %% Classical vs Quantum Logic
-    S1 --> V1{Classical Prediction}
-    T1 --> W1{Quantum Reality}
-    U1 --> X1[Measured Transmission]
-    
-    %% Decision Points
-    V1 --> Y1[Classical Forbidden]
-    W1 --> Z1[Quantum Tunneling]
-    X1 --> AA1[Particle Detection Beyond Barrier]
-    
-    %% Measurement and Detection
-    Y1 --> BB1[Classical Prediction Failure]
-    Z1 --> CC1[Quantum Tunneling Success]
-    AA1 --> DD1[Energy Verification]
-    
-    %% Energy Conservation
-    BB1 --> EE1[Wave Function Collapse]
-    CC1 --> FF1[Final Particle State]
-    DD1 --> GG1[Energy Conservation Check]
-    
-    %% Final Results
-    EE1 --> HH1[Measurement Complete]
-    FF1 --> II1[Quantum Effect Confirmed]
-    GG1 --> JJ1[Energy Conservation Verified]
-    
-    %% Styling - Physics 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 B1 fill:#74c0fc,color:#fff
-    style D1 fill:#74c0fc,color:#fff
-    style F1 fill:#74c0fc,color:#fff
-    style V1 fill:#74c0fc,color:#fff
-    style W1 fill:#74c0fc,color:#fff
-    style X1 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
-    style EE1 fill:#74c0fc,color:#fff
-    style FF1 fill:#74c0fc,color:#fff
-    style GG1 fill:#74c0fc,color:#fff
-    
-    style HH1 fill:#b197fc,color:#fff
-    style II1 fill:#b197fc,color:#fff
-    style JJ1 fill:#b197fc,color:#fff
-            </div>
-            
-            <div style="margin-top: 1rem; display: flex; flex-wrap: wrap; gap: 0.5rem; justify-content: center;">
-                <div style="display:inline-flex; align-items:center; gap:.5rem; padding:.25rem .5rem; border-radius: 999px; border: 1px solid rgba(0,0,0,.08); background:#fff;">
-                    <span style="width: 12px; height: 12px; border-radius: 2px; border:1px solid rgba(0,0,0,.15); background:#ff6b6b;"></span>Energy & Geometric Inputs
-                </div>
-                <div style="display:inline-flex; align-items:center; gap:.5rem; padding:.25rem .5rem; border-radius: 999px; border: 1px solid rgba(0,0,0,.08); background:#fff;">
-                    <span style="width: 12px; height: 12px; border-radius: 2px; border:1px solid rgba(0,0,0,.15); background:#ffd43b;"></span>Wave Functions & Fields
-                </div>
-                <div style="display:inline-flex; align-items:center; gap:.5rem; padding:.25rem .5rem; border-radius: 999px; border: 1px solid rgba(0,0,0,.08); background:#fff;">
-                    <span style="width: 12px; height: 12px; border-radius: 2px; border:1px solid rgba(0,0,0,.15); background:#51cf66;"></span>Quantum Processing
-                </div>
-                <div style="display:inline-flex; align-items:center; gap:.5rem; padding:.25rem .5rem; border-radius: 999px; border: 1px solid rgba(0,0,0,.08); background:#fff;">
-                    <span style="width: 12px; height: 12px; border-radius: 2px; border:1px solid rgba(0,0,0,.15); background:#74c0fc;"></span>Intermediates
-                </div>
-                <div style="display:inline-flex; align-items:center; gap:.5rem; padding:.25rem .5rem; border-radius: 999px; border: 1px solid rgba(0,0,0,.08); background:#fff;">
-                    <span style="width: 12px; height: 12px; border-radius: 2px; border:1px solid rgba(0,0,0,.15); background:#b197fc;"></span>Products
-                </div>
-            </div>
-            
-            <div class="figure-caption">
-                <strong>Figure 1.</strong> Quantum Tunneling Process. This physics process visualization demonstrates quantum mechanical phenomena. The flowchart shows energy inputs, wave functions and fields, quantum processing operations, intermediate calculations, and final measurement outcomes.
-            </div>
+        <div class="overview" style="margin: 2rem 0; padding: 1.5rem; background: #f8f9fa; border-radius: 8px;">
+            <h2>Overview</h2>
+            <p>
+                This collection contains physics process visualizations created using the Programming Framework methodology. 
+                Each process has been analyzed using Large Language Models and represented as interactive Mermaid flowcharts.
+            </p>
         </div>
 
-        <h2>2. Nuclear Fusion Process</h2>
-        <div class="figure">
-            <div class="mermaid">
-graph TD
-    %% Initial Setup
-    %% Input Conditions
-    A2[High Temperature Plasma] --> B2[Thermal Energy Input]
-    C2[High Pressure Environment] --> D2[Pressure Confinement]
-    E2[Deuterium-Tritium Fuel] --> F2[Fuel Preparation]
-    %% Plasma State
-    B2 --> G2[Ionization Process]
-    D2 --> H2[Magnetic Confinement]
-    F2 --> I2[Fuel Injection]
-    %% Fusion Conditions
-    G2 --> J2[Plasma Heating]
-    H2 --> K2[Confinement Stability]
-    I2 --> L2[Fuel Mixing]
-    %% Nuclear Reactions
-    J2 --> M2[Collision Frequency]
-    K2 --> N2[Confinement Time]
-    L2 --> O2[Reaction Rate]
-    %% Fusion Process
-    M2 --> P2[Deuterium-Tritium Collision]
-    N2 --> Q2[Plasma Containment]
-    O2 --> R2[Fusion Cross Section]
-    %% Energy Release
-    P2 --> S2[Helium-4 Formation]
-    Q2 --> T2[Neutron Emission]
-    R2 --> U2[Energy Release]
-    %% Energy Conversion
-    S2 --> V2[Kinetic Energy Transfer]
-    T2 --> W2[Neutron Capture]
-    U2 --> X2[Heat Generation]
-    %% Power Generation
-    V2 --> Y2[Plasma Heating]
-    W2 --> Z2[Breeding Blanket]
-    X2 --> AA2[Steam Generation]
-    %% Final Output
-    Y2 --> BB2[Self-Sustaining Fusion]
-    Z2 --> CC2[Tritium Breeding]
-    AA2 --> DD2[Electrical Power]
-    %% Process Control
-    BB2 --> EE2[Fusion Reactor Operation]
-    CC2 --> FF2[Fuel Cycle Management]
-    DD2 --> GG2[Power Grid Integration]
-    %% Styling - Physics Color Scheme
-    %% Styling - Biological Color Scheme
-    style A2 fill:#ff6b6b,color:#fff
-    style C2 fill:#ff6b6b,color:#fff
-    style E2 fill:#ff6b6b,color:#fff
-    style G2 fill:#ffd43b,color:#000
-    style H2 fill:#ffd43b,color:#000
-    style I2 fill:#ffd43b,color:#000
-    style J2 fill:#ffd43b,color:#000
-    style K2 fill:#ffd43b,color:#000
-    style L2 fill:#ffd43b,color:#000
-    style M2 fill:#51cf66,color:#fff
-    style N2 fill:#51cf66,color:#fff
-    style O2 fill:#51cf66,color:#fff
-    style P2 fill:#51cf66,color:#fff
-    style Q2 fill:#51cf66,color:#fff
-    style R2 fill:#51cf66,color:#fff
-    style S2 fill:#51cf66,color:#fff
-    style T2 fill:#51cf66,color:#fff
-    style U2 fill:#51cf66,color:#fff
-    style V2 fill:#51cf66,color:#fff
-    style W2 fill:#51cf66,color:#fff
-    style X2 fill:#51cf66,color:#fff
-    style B2 fill:#74c0fc,color:#fff
-    style D2 fill:#74c0fc,color:#fff
-    style F2 fill:#74c0fc,color:#fff
-    style Y2 fill:#74c0fc,color:#fff
-    style Z2 fill:#74c0fc,color:#fff
-    style AA2 fill:#74c0fc,color:#fff
-    style BB2 fill:#74c0fc,color:#fff
-    style CC2 fill:#74c0fc,color:#fff
-    style DD2 fill:#74c0fc,color:#fff
-    style EE2 fill:#74c0fc,color:#fff
-    style FF2 fill:#74c0fc,color:#fff
-    style GG2 fill:#74c0fc,color:#fff
-    style HH2 fill:#b197fc,color:#fff
-    style II2 fill:#b197fc,color:#fff
-    style JJ2 fill:#b197fc,color:#fff
-                    </div>
-            
-            <div style="margin-top: 1rem; display: flex; flex-wrap: wrap; gap: 0.5rem; justify-content: center;">
-                <div style="display:inline-flex; align-items:center; gap:.5rem; padding:.25rem .5rem; border-radius: 999px; border: 1px solid rgba(0,0,0,.08); background:#fff;">
-                    <span style="width: 12px; height: 12px; border-radius: 2px; border:1px solid rgba(0,0,0,.15); background:#ff6b6b;"></span>Plasma & Fuel Inputs
-                </div>
-                <div style="display:inline-flex; align-items:center; gap:.5rem; padding:.25rem .5rem; border-radius: 999px; border: 1px solid rgba(0,0,0,.08); background:#fff;">
-                    <span style="width: 12px; height: 12px; border-radius: 2px; border:1px solid rgba(0,0,0,.15); background:#ffd43b;"></span>Confinement Systems
-                </div>
-                <div style="display:inline-flex; align-items:center; gap:.5rem; padding:.25rem .5rem; border-radius: 999px; border: 1px solid rgba(0,0,0,.08); background:#fff;">
-                    <span style="width: 12px; height: 12px; border-radius: 2px; border:1px solid rgba(0,0,0,.15); background:#51cf66;"></span>Nuclear Fusion Reactions
-                </div>
-                <div style="display:inline-flex; align-items:center; gap:.5rem; padding:.25rem .5rem; border-radius: 999px; border: 1px solid rgba(0,0,0,.08); background:#fff;">
-                    <span style="width: 12px; height: 12px; border-radius: 2px; border:1px solid rgba(0,0,0,.15); background:#74c0fc;"></span>Intermediates
-                </div>
-                <div style="display:inline-flex; align-items:center; gap:.5rem; padding:.25rem .5rem; border-radius: 999px; border: 1px solid rgba(0,0,0,.08); background:#fff;">
-                    <span style="width: 12px; height: 12px; border-radius: 2px; border:1px solid rgba(0,0,0,.15); background:#b197fc;"></span>Products
-                </div>
-            </div>
+        <section>
+            <h2>Physics Process Batches</h2>
             
-            <div class="figure-caption">
-                <strong>Figure 2.</strong> Nuclear Fusion Process. This physics process visualization demonstrates nuclear energy production. The flowchart shows plasma inputs, confinement systems, nuclear fusion reactions, intermediate processes, and final energy output.
+            <div class="batch-links">
+                <a href="https://huggingface.co/spaces/garywelz/programming_framework/blob/main/physics_batch_01.html" class="batch-link" target="_blank">
+                    <span class="batch-number">Batch 01</span>
+                    <span class="batch-title">Physics Processes - Batch 1</span>
+                </a>
             </div>
-        </div>
 
-        <h2>3. Electromagnetic Wave Propagation</h2>
-        <div class="figure">
-            <div class="mermaid">
-graph TD
-    %% Initial Setup
-    %% Input Conditions
-    A3[Electromagnetic Source] --> B3[Source Analysis]
-    C3[Medium Properties] --> D3[Medium Analysis]
-    E3[Boundary Conditions] --> F3[Boundary Definition]
-    %% Wave Generation
-    B3 --> G3[Electric Field Generation]
-    D3 --> H3[Dielectric Properties]
-    F3 --> I3[Interface Conditions]
-    %% Wave Propagation
-    G3 --> J3[Maxwell's Equations]
-    H3 --> K3[Wave Speed Calculation]
-    I3 --> L3[Reflection/Refraction]
-    %% Field Evolution
-    J3 --> M3[Electric Field E]
-    K3 --> N3[Magnetic Field B]
-    L3 --> O3[Wave Vector k]
-    %% Wave Dynamics
-    M3 --> P3[Field Oscillation]
-    N3 --> Q3[Energy Density]
-    O3 --> R3[Phase Velocity]
-    %% Energy Transport
-    P3 --> S3[Poynting Vector]
-    Q3 --> T3[Energy Conservation]
-    R3 --> U3[Group Velocity]
-    %% Wave Interaction
-    S3 --> V3[Energy Flux]
-    T3 --> W3[Power Transmission]
-    U3 --> X3[Dispersion Effects]
-    %% Detection
-    V3 --> Y3[Wave Detection]
-    W3 --> Z3[Signal Processing]
-    X3 --> AA3[Interference Patterns]
-    %% Final Results
-    Y3 --> BB3[Wave Amplitude]
-    Z3 --> CC3[Phase Information]
-    AA3 --> DD3[Interference Fringes]
-    %% Output
-    BB3 --> EE3[Electromagnetic Wave Detected]
-    CC3 --> FF3[Phase Information Extracted]
-    DD3 --> GG3[Interference Pattern Analyzed]
-    %% Styling - Physics Color Scheme
-    %% Styling - Biological Color Scheme
-    style A3 fill:#ff6b6b,color:#fff
-    style C3 fill:#ff6b6b,color:#fff
-    style E3 fill:#ff6b6b,color:#fff
-    style G3 fill:#ffd43b,color:#000
-    style H3 fill:#ffd43b,color:#000
-    style I3 fill:#ffd43b,color:#000
-    style J3 fill:#ffd43b,color:#000
-    style K3 fill:#ffd43b,color:#000
-    style L3 fill:#ffd43b,color:#000
-    style M3 fill:#51cf66,color:#fff
-    style N3 fill:#51cf66,color:#fff
-    style O3 fill:#51cf66,color:#fff
-    style P3 fill:#51cf66,color:#fff
-    style Q3 fill:#51cf66,color:#fff
-    style R3 fill:#51cf66,color:#fff
-    style S3 fill:#51cf66,color:#fff
-    style T3 fill:#51cf66,color:#fff
-    style U3 fill:#51cf66,color:#fff
-    style V3 fill:#51cf66,color:#fff
-    style W3 fill:#51cf66,color:#fff
-    style X3 fill:#51cf66,color:#fff
-    style B3 fill:#74c0fc,color:#fff
-    style D3 fill:#74c0fc,color:#fff
-    style F3 fill:#74c0fc,color:#fff
-    style Y3 fill:#74c0fc,color:#fff
-    style Z3 fill:#74c0fc,color:#fff
-    style AA3 fill:#74c0fc,color:#fff
-    style BB3 fill:#74c0fc,color:#fff
-    style CC3 fill:#74c0fc,color:#fff
-    style DD3 fill:#74c0fc,color:#fff
-    style EE3 fill:#74c0fc,color:#fff
-    style FF3 fill:#74c0fc,color:#fff
-    style GG3 fill:#74c0fc,color:#fff
-    style HH3 fill:#b197fc,color:#fff
-    style II3 fill:#b197fc,color:#fff
-    style JJ3 fill:#b197fc,color:#fff
-                    </div>
-            
-            <div style="margin-top: 1rem; display: flex; flex-wrap: wrap; gap: 0.5rem; justify-content: center;">
-                <div style="display:inline-flex; align-items:center; gap:.5rem; padding:.25rem .5rem; border-radius: 999px; border: 1px solid rgba(0,0,0,.08); background:#fff;">
-                    <span style="width: 12px; height: 12px; border-radius: 2px; border:1px solid rgba(0,0,0,.15); background:#ff6b6b;"></span>Source & Medium Inputs
-                </div>
-                <div style="display:inline-flex; align-items:center; gap:.5rem; padding:.25rem .5rem; border-radius: 999px; border: 1px solid rgba(0,0,0,.08); background:#fff;">
-                    <span style="width: 12px; height: 12px; border-radius: 2px; border:1px solid rgba(0,0,0,.15); background:#ffd43b;"></span>Electromagnetic Fields
-                </div>
-                <div style="display:inline-flex; align-items:center; gap:.5rem; padding:.25rem .5rem; border-radius: 999px; border: 1px solid rgba(0,0,0,.08); background:#fff;">
-                    <span style="width: 12px; height: 12px; border-radius: 2px; border:1px solid rgba(0,0,0,.15); background:#51cf66;"></span>Wave Propagation
-                </div>
-                <div style="display:inline-flex; align-items:center; gap:.5rem; padding:.25rem .5rem; border-radius: 999px; border: 1px solid rgba(0,0,0,.08); background:#fff;">
-                    <span style="width: 12px; height: 12px; border-radius: 2px; border:1px solid rgba(0,0,0,.15); background:#74c0fc;"></span>Intermediates
-                </div>
-                <div style="display:inline-flex; align-items:center; gap:.5rem; padding:.25rem .5rem; border-radius: 999px; border: 1px solid rgba(0,0,0,.08); background:#fff;">
-                    <span style="width: 12px; height: 12px; border-radius: 2px; border:1px solid rgba(0,0,0,.15); background:#b197fc;"></span>Products
-                </div>
-            </div>
-            
-            <div class="figure-caption">
-                <strong>Figure 3.</strong> Electromagnetic Wave Propagation. This physics process visualization demonstrates electromagnetic wave dynamics. The flowchart shows source inputs, electromagnetic fields, wave propagation processes, intermediate calculations, and final detection results.
+            <div class="batch-links">
+                <a href="https://huggingface.co/spaces/garywelz/programming_framework/blob/main/physics_batch_02.html" class="batch-link" target="_blank">
+                    <span class="batch-number">Batch 02</span>
+                    <span class="batch-title">Physics Processes - Batch 2</span>
+                </a>
             </div>
-        </div>
+        </section>
 
-        <h2>4. Thermodynamic Cycle Process</h2>
-        <div class="figure">
-            <div class="mermaid">
-graph TD
-    %% Initial Setup
-    %% Input Conditions
-    A4[Heat Source] --> B4[Heat Supply]
-    C4[Working Fluid] --> D4[Fluid Properties]
-    E4[System Boundaries] --> F4[Boundary Definition]
-    %% Initial State
-    B4 --> G4[High Temperature Reservoir]
-    D4 --> H4[Fluid State Analysis]
-    F4 --> I4[System Isolation]
-    %% Isothermal Expansion
-    G4 --> J4[Heat Addition Q1]
-    H4 --> K4[Volume Expansion]
-    I4 --> L4[Work Output W1]
-    %% Adiabatic Expansion
-    J4 --> M4[Temperature Decrease]
-    K4 --> N4[Pressure Reduction]
-    L4 --> O4[Work Output W2]
-    %% Isothermal Compression
-    M4 --> P4[Heat Rejection Q2]
-    N4 --> Q4[Volume Compression]
-    O4 --> R4[Work Input W3]
-    %% Adiabatic Compression
-    P4 --> S4[Temperature Increase]
-    Q4 --> T4[Pressure Increase]
-    R4 --> U4[Work Input W4]
-    %% Cycle Completion
-    S4 --> V4[Return to Initial State]
-    T4 --> W4[System Reset]
-    U4 --> X4[Net Work Output]
-    %% Efficiency Calculation
-    V4 --> Y4[Cycle Efficiency eta]
-    W4 --> Z4[Energy Conservation]
-    X4 --> AA4[Power Generation]
-    %% Final Results
-    Y4 --> BB4[Thermal Efficiency]
-    Z4 --> CC4[Energy Balance]
-    AA4 --> DD4[Mechanical Power]
-    %% Output
-    BB4 --> EE4[Thermodynamic Cycle Complete]
-    CC4 --> FF4[Energy Conversion Efficient]
-    DD4 --> GG4[Power Output Maximized]
-    %% Styling - Physics Color Scheme
-    %% Styling - Biological Color Scheme
-    style A4 fill:#ff6b6b,color:#fff
-    style C4 fill:#ff6b6b,color:#fff
-    style E4 fill:#ff6b6b,color:#fff
-    style G4 fill:#ffd43b,color:#000
-    style H4 fill:#ffd43b,color:#000
-    style I4 fill:#ffd43b,color:#000
-    style J4 fill:#ffd43b,color:#000
-    style K4 fill:#ffd43b,color:#000
-    style L4 fill:#ffd43b,color:#000
-    style M4 fill:#51cf66,color:#fff
-    style N4 fill:#51cf66,color:#fff
-    style O4 fill:#51cf66,color:#fff
-    style P4 fill:#51cf66,color:#fff
-    style Q4 fill:#51cf66,color:#fff
-    style R4 fill:#51cf66,color:#fff
-    style S4 fill:#51cf66,color:#fff
-    style T4 fill:#51cf66,color:#fff
-    style U4 fill:#51cf66,color:#fff
-    style V4 fill:#51cf66,color:#fff
-    style W4 fill:#51cf66,color:#fff
-    style X4 fill:#51cf66,color:#fff
-    style B4 fill:#74c0fc,color:#fff
-    style D4 fill:#74c0fc,color:#fff
-    style F4 fill:#74c0fc,color:#fff
-    style Y4 fill:#74c0fc,color:#fff
-    style Z4 fill:#74c0fc,color:#fff
-    style AA4 fill:#74c0fc,color:#fff
-    style BB4 fill:#74c0fc,color:#fff
-    style CC4 fill:#74c0fc,color:#fff
-    style DD4 fill:#74c0fc,color:#fff
-    style EE4 fill:#74c0fc,color:#fff
-    style FF4 fill:#74c0fc,color:#fff
-    style GG4 fill:#74c0fc,color:#fff
-    style HH4 fill:#b197fc,color:#fff
-    style II4 fill:#b197fc,color:#fff
-    style JJ4 fill:#b197fc,color:#fff
-                    </div>
-            
-            <div style="margin-top: 1rem; display: flex; flex-wrap: wrap; gap: 0.5rem; justify-content: center;">
-                <div style="display:inline-flex; align-items:center; gap:.5rem; padding:.25rem .5rem; border-radius: 999px; border: 1px solid rgba(0,0,0,.08); background:#fff;">
-                    <span style="width: 12px; height: 12px; border-radius: 2px; border:1px solid rgba(0,0,0,.15); background:#ff6b6b;"></span>Heat & Fluid Inputs
-                </div>
-                <div style="display:inline-flex; align-items:center; gap:.5rem; padding:.25rem .5rem; border-radius: 999px; border: 1px solid rgba(0,0,0,.08); background:#fff;">
-                    <span style="width: 12px; height: 12px; border-radius: 2px; border:1px solid rgba(0,0,0,.15); background:#ffd43b;"></span>Thermodynamic Systems
-                </div>
-                <div style="display:inline-flex; align-items:center; gap:.5rem; padding:.25rem .5rem; border-radius: 999px; border: 1px solid rgba(0,0,0,.08); background:#fff;">
-                    <span style="width: 12px; height: 12px; border-radius: 2px; border:1px solid rgba(0,0,0,.15); background:#51cf66;"></span>Thermodynamic Processes
-                </div>
-                <div style="display:inline-flex; align-items:center; gap:.5rem; padding:.25rem .5rem; border-radius: 999px; border: 1px solid rgba(0,0,0,.08); background:#fff;">
-                    <span style="width: 12px; height: 12px; border-radius: 2px; border:1px solid rgba(0,0,0,.15); background:#74c0fc;"></span>Intermediates
-                </div>
-                <div style="display:inline-flex; align-items:center; gap:.5rem; padding:.25rem .5rem; border-radius: 999px; border: 1px solid rgba(0,0,0,.08); background:#fff;">
-                    <span style="width: 12px; height: 12px; border-radius: 2px; border:1px solid rgba(0,0,0,.15); background:#b197fc;"></span>Products
-                </div>
-            </div>
-            
-            <div class="figure-caption">
-                <strong>Figure 4.</strong> Thermodynamic Cycle Process. This physics process visualization demonstrates energy conversion cycles. The flowchart shows heat inputs, thermodynamic systems, thermodynamic processes, intermediate states, and final power output.
+        <div class="navigation">
+            <h3>Navigation</h3>
+            <div class="nav-links">
+                <a href="index.html" class="nav-link">← Back to Programming Framework</a>
+                <a href="https://huggingface.co/spaces/garywelz/programming_framework/blob/main/biology_processes.html" class="nav-link" target="_blank">Biology Processes</a>
+                <a href="https://huggingface.co/spaces/garywelz/programming_framework/blob/main/chemistry_index.html" class="nav-link" target="_blank">Chemistry Processes</a>
+                <a href="https://huggingface.co/spaces/garywelz/programming_framework/blob/main/mathematics_processes.html" class="nav-link" target="_blank">Mathematics Processes</a>
+                <a href="https://huggingface.co/spaces/garywelz/programming_framework/blob/main/computer_science_index.html" class="nav-link" target="_blank">Computer Science Processes</a>
             </div>
         </div>
 
-        <h2>5. Particle Accelerator Process</h2>
-        <div class="figure">
-            <div class="mermaid">
-graph TD
-    %% Initial Setup
-    %% Input Conditions
-    A5[Particle Source] --> B5[Source Analysis]
-    C5[Accelerating Fields] --> D5[Field Generation]
-    E5[Beam Optics] --> F5[Optics Setup]
-    %% Particle Preparation
-    B5 --> G5[Particle Generation]
-    D5 --> H5[Electric Field E]
-    F5 --> I5[Magnetic Field B]
-    %% Initial Acceleration
-    G5 --> J5[Particle Injection]
-    H5 --> K5[Linear Acceleration]
-    I5 --> L5[Beam Focusing]
-    %% Acceleration Process
-    J5 --> M5[Velocity Increase]
-    K5 --> N5[Energy Gain]
-    L5 --> O5[Beam Confinement]
-    %% Circular Motion
-    M5 --> P5[Centripetal Force]
-    N5 --> Q5[Relativistic Effects]
-    O5 --> R5[Orbital Motion]
-    %% Energy Build-up
-    P5 --> S5[Radius of Curvature]
-    Q5 --> T5[Mass Increase]
-    R5 --> U5[Angular Velocity]
-    %% Beam Dynamics
-    S5 --> V5[Beam Stability]
-    T5 --> W5[Energy Synchronization]
-    U5 --> X5[Revolution Frequency]
-    %% Collision Process
-    V5 --> Y5[Beam Crossing]
-    W5 --> Z5[Particle Collisions]
-    X5 --> AA5[Reaction Products]
-    %% Detection
-    Y5 --> BB5[Collision Detection]
-    Z5 --> CC5[Particle Tracking]
-    AA5 --> DD5[Energy Measurement]
-    %% Final Results
-    BB5 --> EE5[Collision Events]
-    CC5 --> FF5[Particle Trajectories]
-    DD5 --> GG5[Energy Distribution]
-    %% Output
-    EE5 --> HH5[Particle Accelerator Active]
-    FF5 --> II5[Beam Dynamics Analyzed]
-    GG5 --> JJ5[Physics Data Collected]
-    %% Styling - Physics Color Scheme
-    %% Styling - Biological Color Scheme
-    style A5 fill:#ff6b6b,color:#fff
-    style C5 fill:#ff6b6b,color:#fff
-    style E5 fill:#ff6b6b,color:#fff
-    style G5 fill:#ffd43b,color:#000
-    style H5 fill:#ffd43b,color:#000
-    style I5 fill:#ffd43b,color:#000
-    style J5 fill:#ffd43b,color:#000
-    style K5 fill:#ffd43b,color:#000
-    style L5 fill:#ffd43b,color:#000
-    style M5 fill:#51cf66,color:#fff
-    style N5 fill:#51cf66,color:#fff
-    style O5 fill:#51cf66,color:#fff
-    style P5 fill:#51cf66,color:#fff
-    style Q5 fill:#51cf66,color:#fff
-    style R5 fill:#51cf66,color:#fff
-    style S5 fill:#51cf66,color:#fff
-    style T5 fill:#51cf66,color:#fff
-    style U5 fill:#51cf66,color:#fff
-    style V5 fill:#51cf66,color:#fff
-    style W5 fill:#51cf66,color:#fff
-    style X5 fill:#51cf66,color:#fff
-    style B5 fill:#74c0fc,color:#fff
-    style D5 fill:#74c0fc,color:#fff
-    style F5 fill:#74c0fc,color:#fff
-    style Y5 fill:#74c0fc,color:#fff
-    style Z5 fill:#74c0fc,color:#fff
-    style AA5 fill:#74c0fc,color:#fff
-    style BB5 fill:#74c0fc,color:#fff
-    style CC5 fill:#74c0fc,color:#fff
-    style DD5 fill:#74c0fc,color:#fff
-    style EE5 fill:#74c0fc,color:#fff
-    style FF5 fill:#74c0fc,color:#fff
-    style GG5 fill:#74c0fc,color:#fff
-    style HH5 fill:#b197fc,color:#fff
-    style II5 fill:#b197fc,color:#fff
-    style JJ5 fill:#b197fc,color:#fff
-                    </div>
-            
-            <div style="margin-top: 1rem; display: flex; flex-wrap: wrap; gap: 0.5rem; justify-content: center;">
-                <div style="display:inline-flex; align-items:center; gap:.5rem; padding:.25rem .5rem; border-radius: 999px; border: 1px solid rgba(0,0,0,.08); background:#fff;">
-                    <span style="width: 12px; height: 12px; border-radius: 2px; border:1px solid rgba(0,0,0,.15); background:#ff6b6b;"></span>Particle & Field Inputs
-                </div>
-                <div style="display:inline-flex; align-items:center; gap:.5rem; padding:.25rem .5rem; border-radius: 999px; border: 1px solid rgba(0,0,0,.08); background:#fff;">
-                    <span style="width: 12px; height: 12px; border-radius: 2px; border:1px solid rgba(0,0,0,.15); background:#ffd43b;"></span>Accelerating Fields
-                </div>
-                <div style="display:inline-flex; align-items:center; gap:.5rem; padding:.25rem .5rem; border-radius: 999px; border: 1px solid rgba(0,0,0,.08); background:#fff;">
-                    <span style="width: 12px; height: 12px; border-radius: 2px; border:1px solid rgba(0,0,0,.15); background:#51cf66;"></span>Acceleration Processes
-                </div>
-                <div style="display:inline-flex; align-items:center; gap:.5rem; padding:.25rem .5rem; border-radius: 999px; border: 1px solid rgba(0,0,0,.08); background:#fff;">
-                    <span style="width: 12px; height: 12px; border-radius: 2px; border:1px solid rgba(0,0,0,.15); background:#74c0fc;"></span>Intermediates
-                </div>
-                <div style="display:inline-flex; align-items:center; gap:.5rem; padding:.25rem .5rem; border-radius: 999px; border: 1px solid rgba(0,0,0,.08); background:#fff;">
-                    <span style="width: 12px; height: 12px; border-radius: 2px; border:1px solid rgba(0,0,0,.15); background:#b197fc;"></span>Products
-                </div>
-            </div>
-            
-            <div class="figure-caption">
-                <strong>Figure 5.</strong> Particle Accelerator Process. This physics process visualization demonstrates particle acceleration mechanisms. The flowchart shows particle inputs, accelerating fields, acceleration processes, intermediate states, and final collision data.
+        <div class="footer">
+            <p><strong>Generated using the Programming Framework methodology</strong></p>
+            <p>Each flowchart preserves maximum detail through optimized Mermaid configuration</p>
+            <div class="contact-info">
+                <p><strong>Gary Welz</strong></p>
+                <p>Retired Faculty Member</p>
+                <p>John Jay College, CUNY (Department of Mathematics and Computer Science)</p>
+                <p>Borough of Manhattan Community College, CUNY</p>
+                <p>CUNY Graduate Center (New Media Lab)</p>
+                <p>Email: gwelz@jjay.cuny.edu</p>
             </div>
         </div>
-
-        <p><strong>Generated using the Programming Framework methodology</strong></p>
-        
-        <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>
 </body>
-</html> 
+</html>
+