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Genome Logic Modeling Project

A Microscope for Biological Processes

GLMP applies the Programming Framework to visualize complex biochemical processes as interactive flowcharts, revealing the logic of life at the molecular level.

📚 Prior Work & Research Contributions

Overview

The Genome Logic Modeling Project (GLMP) represents prior work that demonstrates the first successful application of the Programming Framework to biological process visualization. This research establishes a novel methodology for transforming complex biochemical processes into structured, interactive visual flowcharts using LLM-powered analysis and Mermaid visualization technology.

🔬 Research Contributions

  • • Biological Process Visualization: 50+ processes mapped across 6 major categories
  • • LLM-Powered Analysis: Automated extraction using Google Gemini 2.0 Flash
  • • Interactive Visualization: Mermaid.js-based dynamic flowchart system
  • • Knowledge Engine Integration: Links to Copernicus AI and Programming Framework

⚙️ Technical Achievements

  • • Structured Database: JSON format in Google Cloud Storage
  • • Process Coverage: Central Dogma, Metabolism, Signaling, Proteins, Photosynthesis, DNA Repair
  • • Scalable Architecture: GCS-based storage with web viewer integration
  • • Metadata-Rich Format: Categories, versions, references, source papers

🎯 Position Within CopernicusAI Knowledge Engine

GLMP serves as a specialized application component of the CopernicusAI Knowledge Engine, demonstrating how the Programming Framework can be applied to domain-specific scientific visualization. It integrates with:

  • • Programming Framework (meta-tool)
  • • Copernicus AI (main knowledge engine)
  • • Research Papers Metadata Database
  • • Science Video Database
  • • Multi-modal learning integration

This work establishes a proof-of-concept for domain-specific applications of the Programming Framework, demonstrating its utility in biological sciences and potential for extension to other scientific disciplines.

50+
Biological Processes
JSON
Flowchart Format
LLM
AI-Powered Analysis
Mermaid
Visualization Engine

🔬 What is GLMP?

The Genome Logic Modeling Project is the first specialized application of the Programming Framework to the domain of biology. It transforms complex biochemical processes into clear, visual flowcharts that reveal the step-by-step logic underlying life's molecular machinery.

🎯 Purpose

Break down biological complexity into understandable visual logic, making advanced biochemistry accessible to researchers, students, and AI systems.

⚙️ How It Works

LLMs analyze scientific literature to extract process steps, decision points, and molecular interactions, then encode them as Mermaid flowcharts stored in JSON.

📊 GLMP Database

Access the interactive GLMP database table with all available biological processes, metadata, and analysis.

🧬 Open GLMP Database Table

📚 Process Database

🧬 Central Dogma

  • • DNA Replication
  • • Transcription
  • • Translation
  • • RNA Processing
  • • Post-translational Modifications

⚡ Metabolic Pathways

  • • Glycolysis
  • • Krebs Cycle (TCA)
  • • Oxidative Phosphorylation
  • • Gluconeogenesis
  • • Pentose Phosphate Pathway

📡 Cell Signaling

  • • MAPK Pathway
  • • PI3K/AKT Pathway
  • • Wnt Signaling
  • • Notch Pathway
  • • JAK-STAT Pathway

🔄 Protein Processes

  • • Protein Folding
  • • Ubiquitination
  • • Autophagy
  • • Proteasome Degradation
  • • Chaperone Systems

🌱 Photosynthesis

  • • Light Reactions
  • • Calvin Cycle
  • • C4 Pathway
  • • CAM Photosynthesis
  • • Photorespiration

🔧 DNA Repair

  • • Base Excision Repair
  • • Nucleotide Excision Repair
  • • Mismatch Repair
  • • Double-strand Break Repair
  • • Direct Repair
📦 View Archived Processes (v1.0) →

🚀 How to Use GLMP

1️⃣

Select Process

Choose a biological process from the viewer above or browse the database

2️⃣

View Flowchart

Explore the interactive Mermaid visualization showing each step and decision point

3️⃣

Learn & Integrate

Use for education, research, or integrate with Copernicus AI podcasts

📦 Archived Versions

Earlier versions of GLMP processes and experimental visualizations

View Archive

🔗 Related Projects

🛠️ Programming Framework

The meta-tool that powers GLMP. A universal method for process analysis across any discipline.

Explore Framework →

🔬 Copernicus AI

Knowledge engine that integrates GLMP visualizations with AI-generated scientific podcasts.

Visit Copernicus AI →

How to Cite This Work

Welz, G. (2024–2025). Genome Logic Modeling Project (GLMP).
Hugging Face Spaces. https://huggingface.co/spaces/garywelz/glmp

This project serves as a testbed for integrating AI systems into scientific reasoning pipelines, enabling both human and AI agents to analyze, compare, and extend biological knowledge structures.

GLMP is designed as infrastructure for AI-assisted science, not as a static visualization collection.