A comprehensive bioinformatics platform built with modern technologies in a monorepo structure.

openbiocure-platform-ui/
├── backend/                 # FastAPI Python backend
│   ├── app/                # Application modules
│   │   ├── api/           # API endpoints
│   │   ├── core/          # Core configuration
│   │   ├── models/        # Database models
│   │   ├── schemas/       # Pydantic schemas
│   │   ├── services/      # Business logic
│   │   └── utils/         # Utility functions
│   ├── tests/             # Test suite
│   ├── venv/              # Python virtual environment
│   ├── main.py            # FastAPI application entry point
│   └── requirements.txt   # Python dependencies
├── frontend/               # Frontend applications
│   ├── shell-app/         # React shell application (main container)
│   ├── research-core-app/ # Research core micro frontend
│   ├── analysis-app/      # Analysis micro frontend
│   ├── workflow-app/      # Workflow micro frontend
│   └── shared/            # Shared components and utilities
├── docs/                   # Documentation
│   └── models.md          # Data models and API documentation
└── README.md              # This file

• Python 3.9+
• Node.js 18+
• npm or yarn

1. Navigate to backend directory:

   cd backend

2. Create and activate virtual environment:

   python3 -m venv venv
   source venv/bin/activate  # On Windows: venv\Scripts\activate

3. Install dependencies:

   pip install -r requirements.txt

4. Run the FastAPI server:

   python main.py
   # or
   uvicorn main:app --reload

5. Access the API:

   • API: http://localhost:8000
   • Interactive docs: http://localhost:8000/docs
   • Alternative docs: http://localhost:8000/redoc

1. Install all dependencies:

   cd frontend
   npm run install:all

2. Start all micro frontends:

   npm run dev

3. Start individual applications:

   npm run start:shell      # Port 3000 (Main app)
   npm run start:research-core # Port 3001
   npm run start:analysis   # Port 3002
   npm run start:workflow   # Port 3003

4. Access the applications:

   • Shell App: http://localhost:3000
   • Research Core: http://localhost:3001
   • Analysis: http://localhost:3002
   • Workflow: http://localhost:3003

The backend is built with FastAPI and follows a modular architecture:

• API Routes: RESTful endpoints in app/api/
• Data Models: SQLAlchemy models in app/models/
• Schemas: Pydantic validation schemas in app/schemas/
• Services: Business logic in app/services/
• Core: Configuration and utilities in app/core/

The frontend uses a React-based micro frontend architecture with modern UI components:

• React 18: Modern React with hooks and functional components
• Micro Frontends: Independent applications for different domains
• Module Federation: Seamless component sharing between apps
• Modern Tooling: Create React App, TypeScript, ESLint
• UI Components: shadcn/ui for professional, accessible, and customizable components
• Design System: Montserrat typography with professional color palette (blues, orange, cyan)
• Performance: Lazy loading, independent deployment, better caching

The API provides endpoints for:

• Authentication: User registration, login, JWT tokens
• Users: Profile management
• Bio Samples: Sample tracking and management
• Analyses: Analysis workflows and results

See docs/models.md for detailed API specifications and data models.

Comprehensive feature breakdown with user stories and requirements:

• Feature Epics: Detailed breakdown of platform capabilities
• User Stories: Implementation requirements and acceptance criteria
• Development Roadmap: MVP and Phase 2 feature priorities

See docs/features/README.md for the complete feature breakdown.

Complete visual identity and component guidelines:

• Color Palette: Professional blues, orange, and cyan scheme
• Typography: Montserrat font family with comprehensive scale
• Component Guidelines: Button, form, and navigation standards
• Accessibility: Color contrast and focus indicator requirements

See docs/design-system.md for the complete design specifications.

• python main.py - Run FastAPI server
• uvicorn main:app --reload - Run with auto-reload
• pytest - Run test suite

• npm run dev - Start all micro frontends
• npm run start:shell - Start shell application
• npm run start:research-core - Start research core app
• npm run start:analysis - Start analysis app
• npm run start:workflow - Start workflow app
• npm run build - Build all applications
• npm run test - Run tests across all apps

Create .env files in respective directories:

DATABASE_URL=postgresql://user:password@localhost/dbname
SECRET_KEY=your-secret-key
ALGORITHM=HS256
ACCESS_TOKEN_EXPIRE_MINUTES=30

REACT_APP_API_URL=http://localhost:8000
REACT_APP_SHELL_URL=http://localhost:3000
REACT_APP_RESEARCH_CORE_URL=http://localhost:3001
REACT_APP_ANALYSIS_URL=http://localhost:3002
REACT_APP_WORKFLOW_URL=http://localhost:3003

1. Create a feature branch
2. Make your changes
3. Add tests if applicable
4. Ensure all tests pass
5. Submit a pull request

This project is licensed under the MIT License.

For support and questions, please open an issue in the repository.