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.
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.
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:
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.
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.
Break down biological complexity into understandable visual logic, making advanced biochemistry accessible to researchers, students, and AI systems.
LLMs analyze scientific literature to extract process steps, decision points, and molecular interactions, then encode them as Mermaid flowcharts stored in JSON.
Full-title HTML manuscripts (Google Cloud Storage):
Teaching (April 2026): Flowcharts, Mermaid & smarter perturbation design — guest seminar slide deck (Prof. Konstantinos Krampis, CUNY BIO 37105 / 77105).
Companion article (HTML): Mermaid Flowcharts and Smarter Perturbation Design — expanded notes, hands-on preface, and references aligned with the deck.
The first paper positions GLMP’s regulatory flowcharts alongside the public Algorithms and Axiomatic Theories corpus (algorithms plus axiomatic dependency graphs). Same Mermaid idiom; distinct public indices.
Use this Space for interactive exploration; use the GLMP database table for sortable metadata, export, and deep links to each flowchart.
The public summary table lists GLMP processes with organism, category, graph statistics (nodes, conditionals, logic gates, loops), and links into interactive viewers. It is the authoritative index for the regulatory-process corpus hosted on Google Cloud Storage.
🧬 Open GLMP Database TableChoose a biological process from the viewer above or browse the database
Explore the interactive Mermaid visualization showing each step and decision point
Use for education, research, or integrate with CopernicusAI podcasts
The meta-tool that powers GLMP. A universal method for process analysis across any discipline.
Explore Framework →Public mathematics database: procedural algorithms and axiomatic dependency graphs—paired conceptually with GLMP in the 2026 typology paper.
Open mathematics table →Knowledge engine that integrates GLMP visualizations with AI-generated scientific podcasts.
Visit CopernicusAI →
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.