Version: 1.0.0
Date: November 2025
Developers: Jeff Osborne and Cursor AI
Location: Manchester University, North Manchester, Indiana, USA
enviPath Integration: Real-time synchronization with the EAWAG-BBD package from envipath.org, providing access to 1,399 compounds, 1,480 reactions (1,301 with enzyme names and EC numbers), and 219 biodegradation pathways.
Pathway Visualization: Interactive graph visualization using Cytoscape.js with hierarchical layout algorithms (Dagre) to display complex biodegradation pathways.
Chemical Structure Processing: RDKit-based molecular structure rendering with automatic SVG generation for compound visualization, plus substructure searching capabilities.
User Workspace: Multi-user system with isolated workspaces where users can create, edit, and manage their own compounds, reactions, and pathways.
Pathway Builder: Interactive drag-and-drop interface for building custom biodegradation pathways with real-time visualization.
Data Caching: Local SQLite database cache for fast access to enviPath data with incremental update capabilities.
Browse enviPath Database: Access the complete EAWAG-BBD package with searchable compounds, reactions, and pathways.
Interactive Pathway Visualization: Explore biodegradation pathways with clickable compounds and reactions, showing detailed information in modals.
Pathway Builder: Create custom pathways by adding compounds and connecting them with reactions using an intuitive graph interface.
Chemical Structure Editor: Draw chemical structures using Ketcher editor, with automatic SMILES generation and SVG rendering.
Structure-Based Search: Search for compounds and pathways by drawing chemical structures. The system uses RDKit to find all compounds containing your drawn structure as a substructure.
Enzyme Information: Reactions include enzyme names and EC numbers extracted from the enviPath database, with links to BRENDA, KEGG, and ExPASy databases.
External Database Links: Direct links to PubChem for compounds, and BRENDA, KEGG, and ExPASy for enzyme information, providing seamless access to additional resources.
User Workspace: Registered users can create, edit, and manage their own compounds, reactions, and pathways.
Rich Text Formatting: Support for HTML formatting in pathway descriptions including links, italics, superscript, subscript, and Greek letters.
Admin Interface: Comprehensive admin dashboard for cache management and user workspace access.
Multi-User Support: Session-based authentication with isolated user workspaces.
Responsive Design: Modern, mobile-friendly interface with consistent styling.
Backend: Python with FastAPI framework for high-performance async API endpoints.
Database: SQLite with SQLAlchemy ORM for data persistence and query optimization.
Chemistry Library: RDKit for molecular structure processing, SMILES parsing, and SVG generation.
Frontend: HTML5, CSS3, JavaScript (ES6+) with Jinja2 templating.
Visualization: Cytoscape.js for interactive graph visualization with Dagre layout algorithm.
Structure Editor: Ketcher standalone editor embedded via iframe with postMessage API communication for drawing and searching chemical structures.
Substructure Search: RDKit-based substructure matching for finding compounds and pathways containing specific chemical moieties.
HTTP Client: httpx for async communication with enviPath REST API.
Authentication: JWT tokens for admin access, session-based authentication for regular users.
Server: Gunicorn with Uvicorn workers, served behind Apache reverse proxy.
enviPath API: envipath.org - Environmental biotransformation pathway database
EAWAG-BBD Package: Package ID: 32de3cf4-e3e6-4168-956e-32fa5ddb0ce1
API Documentation: enviPath REST API Documentation
External Database Links: The system provides direct links to multiple external databases:
For questions, bug reports, or feature requests, please contact Jeff Osborne.
Email: jposborne@manchester.edu
Homepage: https://users.manchester.edu/Facstaff/JPOsborne/index.htm