feat: add BNGL visualization support for biomodels

[androemeda]

Description

This PR integrates the bnglViz library into VCell-AI to provide interactive visualization of BNGL (BioNetGen Language) content for biomodels that support BNGL export. The visualization displays molecular types, species, observables, and reaction rules in an easy-to-understand graphical format.

Note: This PR is raised as part of GSoC proposal preparation to demonstrate that bnglViz can be successfully integrated into VCell-AI. The full implementation planned for GSoC includes deeper integration — specifically, exposing BNGL visualization as a tool in the chat interface so the LLM can trigger it contextually when a user asks to visualize a model's structure. That is documented in the proposal.

---

Implementation Details

Backend Changes

New Service Function (databases_service.py)

• Added get_bngl_file() function that calls VCell's BNGL API endpoint
• Returns empty string when BNGL content is unavailable for a model
• Includes proper error handling

New REST Endpoint (vcelldb_router.py)

• GET /biomodel/{biomodel_id}/biomodel.bngl
• Consistent with existing .vcml and .sbml endpoints
• Returns JSON format: {"data": "<bngl_content>"}

Frontend Changes

bnglViz Integration (frontend/public/bnglviz/)

• Copied core JavaScript files: html-interface.js, bngl-extractor.js, model-graphics.js
• Created minimal iframe HTML with postMessage communication
• Preserved original bnglViz functionality

React Component (BnglVisualizerSection.tsx)

• Fetches BNGL data from backend endpoint
• Iframe-based integration keeps bnglViz isolated from the parent page
• BNGL text is passed to the iframe via postMessage

Page Integration (app/search/[bmid]/page.tsx)

• Added component after the biomodel diagram in the overview tab
• Follows existing design patterns and styling

---

Video Demo

Screen.Recording.2026-03-27.at.3.10.03.PM.mov

---

How to Test

Test Steps:

1. Test a model with BNGL support (should show visualization):
   Navigate to a biomodel page — e.g. any of mblinov's public models

   http://localhost:3000/search/303803335

Expected: BNGL Visualization section appears after the diagram

2. Test API endpoint directly:

   # Model with BNGL support - should return BNGL content
   curl http://localhost:8000/biomodel/{biomodel_id}/biomodel.bngl

---

Technical Notes

• Visualization gracefully degrades — no error shown when BNGL is unavailable
• No breaking changes to existing functionality