Escher Maps for BiGG Models

This repository hosts a comprehensive collection of metabolic maps generated for models in the BiGG Models database. These maps are formatted for Escher and are designed to provide clear, orthogonal visualizations of complex metabolic networks.

🚀 How to Use

You can view and interact with these maps directly using the custom Escher viewer:

👉 Open Escher Viewer

1. Select a Model: Browse the folders in this repository to find the organism/model of interest (e.g., e_coli_core).
2. Choose a View:
   • Combined Map (*_Combined.json): View the entire network tiled by subsystem.
   • Subsystem Map (*_Glycolysis.json): View a focused, individual pathway.
3. Load in Escher: Use the "Load Map" feature on the website to import the JSON file.

🛠️ How it is Generated

These maps were created using an advanced AutoLayout AI pipeline developed by Tianyu Wu. The generation process prioritizes biological clarity and geometric precision:

1. Biological Decomposition:

   • The full network is broken down into meaningful functional units.
   • Priority is given to KEGG Pathways and explicit subsystems.
   • Large clusters are recursively partitioned to ensure readability.

2. Algorithmic Layout:

   • Simulated Annealing: Optimizes node positions to minimize energy (edge crossings, stress).
   • Manhattan Geometry: Enforces strict horizontal and vertical alignment for all edges.
   • Collision Resolution: Active algorithms ensure nodes do not overlap.

3. Smart Labeling:

   • Dynamic collision detection ensures text labels never obscure the network structure.
   • Labels shift adaptively to avoid crossing edges or nodes.

📂 Repository Structure

• {Model_ID}/ - Folder for a specific BiGG model.
  • {Model_ID}_Combined.json - The master map containing all subsystems tiled together.
  • {Model_ID}_{Subsystem}.json - Individual maps for each specific subsystem.

---

Created by Tianyu Wu (GitHub: forxhunter)