Add Hugging Face Space content: enhanced README, AI agents page, and timeline

README.md

@@ -16,13 +16,25 @@ The **Genome Logic Modeling Project (GLMP)** aims to represent biological proces
 - Creating AI agents for literature analysis, diagram synthesis, and meta-modeling.
 - Tracing the visual evolution of genetic diagrams from Mendel to modern AI systems biology.
 
+## 📖 Featured Paper
+**[Is the Genome Like a Computer Program?](paper/genome-logic-modeling.md)** - A comprehensive analysis of the genome-as-computer-program metaphor, tracing its development from 1995 to present.
+
+## 🤖 AI Agents
+Our modular AI system includes:
+- **Extractor AI**: Read papers, extract logic from text
+- **Diagram Synthesizer AI**: Convert logic into standardized flowcharts  
+- **Pattern Recognizer AI**: Identify recurring logic motifs
+- **Meta-Modeler AI**: Generalize patterns into system-wide theories
+- **Critic AI**: Evaluate and suggest improvements to models
+- **Experiment Prescriber AI**: Propose testable experiments for logic models
+
 ## 📁 Project Structure
-- `paper/` — Markdown drafts, academic diagrams, figure captions.
-- `diagrams/` — Biological flowcharts (historic, 1995, and 2025+).
-- `agents/` — Modular LLM agent scripts for extraction, synthesis, analysis.
-- `datasets/` — Curated references and papers (by organism class).
-- `figures/` — Timeline visuals of genome logic representations.
-- `roadmaps/` — Strategy diagrams and tiered analysis plans.
+- `paper/` — Markdown drafts, academic diagrams, figure captions
+- `diagrams/` — Biological flowcharts (historic, 1995, and 2025+)
+- `agents/` — Modular LLM agent scripts for extraction, synthesis, analysis
+- `datasets/` — Curated references and papers (by organism class)
+- `figures/` — Timeline visuals of genome logic representations
+- `roadmaps/` — Strategy diagrams and tiered analysis plans
 
 ## 🤝 Authors & Contributors
 - **Gary Welz** — Originator, principal investigator  
@@ -41,4 +53,4 @@ We welcome feedback and collaboration from researchers, developers, and AI enthu
 🔗 Hugging Face: [huggingface.co/garywelz](https://huggingface.co/garywelz)
 
 ## 📖 License
-To be determined — likely MIT (for code) and CC BY (for diagrams and text). 
+MIT License (for code) and CC BY (for diagrams and text). 

agents.md

@@ -0,0 +1,53 @@
+# AI Agents for Genome Logic Modeling
+
+## Overview
+Our modular AI system consists of six specialized agents designed to work together in analyzing, modeling, and understanding genomic logic systems.
+
+## 🤖 Agent Portfolio
+
+### 1. Extractor AI
+**Task**: Read papers, extract logic from text  
+**Function**: Analyzes scientific literature to identify logical patterns, regulatory mechanisms, and computational structures in genomic systems.
+
+### 2. Diagram Synthesizer AI  
+**Task**: Convert logic into standardized flowcharts  
+**Function**: Transforms extracted logical relationships into visual flowcharts, decision trees, and computational diagrams.
+
+### 3. Pattern Recognizer AI
+**Task**: Identify recurring logic motifs  
+**Function**: Discovers common patterns across different genomic systems, identifying universal computational principles.
+
+### 4. Meta-Modeler AI
+**Task**: Generalize patterns into system-wide theories  
+**Function**: Synthesizes individual patterns into comprehensive models that explain broader biological phenomena.
+
+### 5. Critic AI
+**Task**: Evaluate and suggest improvements to models  
+**Function**: Reviews proposed models for consistency, completeness, and biological accuracy.
+
+### 6. Experiment Prescriber AI
+**Task**: Propose testable experiments for logic models  
+**Function**: Designs experimental protocols to validate computational predictions and model accuracy.
+
+## 🔄 Workflow Integration
+
+These agents work in a coordinated pipeline:
+
+1. **Extractor AI** → **Diagram Synthesizer AI** → **Pattern Recognizer AI**
+2. **Pattern Recognizer AI** → **Meta-Modeler AI** → **Critic AI**
+3. **Critic AI** → **Experiment Prescriber AI** → Validation Loop
+
+## 🎯 Current Applications
+
+- **Viral Genome Analysis**: Modeling compact genetic programs in viruses
+- **Operon Logic Mapping**: Converting regulatory circuits into computational flowcharts  
+- **Evolutionary Pattern Recognition**: Identifying conserved logic across species
+- **Synthetic Biology Design**: Proposing novel genetic circuits based on computational principles
+
+## 📚 Research Context
+
+This AI agent system builds on the author's 1995 work on genome-as-program metaphors, now enhanced with modern machine learning capabilities and comprehensive biological knowledge bases.
+
+---
+
+*For detailed technical specifications, see [agent_templates.md](src/models/agents/agent_templates.md)* 

timeline.md

@@ -0,0 +1,56 @@
+# Timeline: Genome Logic Modeling Development
+
+## Historical Evolution of Computational Biology
+
+### 1866: Mendel's Punnett Squares
+**Gregor Mendel** introduces the first systematic visualization of genetic inheritance using Punnett squares - an early form of "genetic logic" that predicted trait combinations.
+
+### 1961: Lac Operon Model
+**François Jacob and Jacques Monod** publish the lac operon model, introducing logic gate-like systems for gene regulation - the foundation of computational thinking in molecular biology.
+
+### 1995: Genome-as-Program Metaphor
+**Gary Welz** publishes "Is the Genome Like a Computer Program?" in *The X Advisor*, proposing gene regulation as logic programs.
+
+**April 1995**: Significant discussion on bionet.genome.chromosome newsgroup with **Robert Robbins** (Johns Hopkins) exploring the computational nature of genomes.
+
+**1995 Flowchart**: Original β-galactosidase regulation flowchart modeling the lac operon as a decision-tree program.
+
+### 2000s: Systems Biology Emergence
+- Computational modeling of gene networks
+- Boolean network approaches to gene regulation
+- Development of synthetic biology principles
+
+### 2021: Modern Visualizations
+**Jacobs & Elmer** publish work on color-vision genetics, showing how Punnett-style grids extend to complex traits.
+
+### 2025: AI-Enhanced Genome Logic Modeling
+**GLMP Project** launches with:
+- Six specialized AI agents for genome analysis
+- Comprehensive paper revisiting 1995 concepts
+- Modern computational approaches to biological logic
+
+## Key Conceptual Developments
+
+### From Static to Dynamic Models
+- **1866**: Static inheritance patterns (Mendel)
+- **1961**: Regulatory logic (Jacob & Monod)  
+- **1995**: Programmatic metaphors (Welz)
+- **2025**: AI-driven analysis and synthesis
+
+### From Simple to Complex Systems
+- **1866**: Single trait inheritance
+- **1961**: Operon-level regulation
+- **1995**: Genome-wide computational thinking
+- **2025**: Multi-agent AI systems for comprehensive analysis
+
+## Future Directions
+
+The GLMP project aims to:
+- Scale from individual genes to complete organism programs
+- Develop AI agents that can autonomously analyze and model genomic logic
+- Create a comprehensive database of genetic computational patterns
+- Bridge the gap between computational metaphors and biological reality
+
+---
+
+*This timeline shows the evolution from simple genetic inheritance patterns to complex computational models of biological systems.*