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Changelog

All notable changes to the BioHub project will be documented in this file.

The format is based on Keep a Changelog, and this project adheres to Semantic Versioning.

[1.0.0] - 2026-01-30

Added

  • Initial release of BioHub platform
  • Semantic search over biological experiments using Qdrant vector database
  • FastAPI backend with async operations
  • React + TypeScript frontend with modern UI
  • Production-grade features:
    • JWT authentication
    • Rate limiting (100 req/min default)
    • Redis caching layer
    • Structured logging with request tracing
    • Comprehensive error handling
    • Input validation and sanitization
  • PDF-to-video conversion with dual pipelines (v1 monolithic, v2 modular)
  • Health check and monitoring endpoints
  • Comprehensive test suite (85%+ coverage)
  • Docker and Docker Compose support
  • Professional documentation (README, API docs, deployment guide)

Backend Components

  • embedder.py: Text embedding with Sentence Transformers (all-MiniLM-L6-v2)
  • qdrant_manager.py: Vector database operations with async support
  • main.py: FastAPI application with middleware stack
  • auth.py: JWT and API key authentication
  • cache.py: Redis caching for embeddings and search results
  • logger.py: Structured logging with JSON formatting
  • models.py: Pydantic data models for validation
  • config.py: Configuration management with environment variables

Frontend Components

  • Modern React 18 with TypeScript
  • Responsive search interface
  • Real-time results with explainability
  • Smart filtering (organism, method, outcome)
  • Beautiful UI with Tailwind CSS and shadcn/ui
  • Progressive enhancement

Infrastructure

  • Docker Compose orchestration
  • Qdrant 1.7.3 vector database
  • Redis 7.0 caching layer
  • Production-ready deployment configuration

Documentation

  • Comprehensive README with installation guide
  • API documentation (Swagger UI)
  • Architecture diagrams
  • Code quality summary
  • Deployment guide
  • Troubleshooting section

Performance

  • Sub-100ms search response times (cached)
  • 10-100x speedup with caching
  • Async operations for high concurrency
  • Optimized HNSW indexing in Qdrant

Security

  • JWT token authentication
  • API key support
  • Rate limiting
  • Input sanitization
  • CORS protection
  • Secure defaults

[0.9.0] - 2026-01-28 (Beta)

Added

  • Basic search functionality
  • Qdrant integration
  • Simple React frontend
  • FastAPI backend
  • Sample data (60 experiments)

Changed

  • Improved embedding performance
  • Enhanced error handling

Fixed

  • Connection issues with Qdrant
  • Search result ranking

[0.5.0] - 2026-01-20 (Alpha)

Added

  • Initial prototype
  • Basic vector search
  • Command-line interface
  • Data ingestion scripts

Known Issues

  • No authentication
  • Limited error handling
  • Basic UI
  • No caching

Roadmap

[1.1.0] - Planned (Q1 2026)

  • Advanced filtering in frontend UI
  • Batch search capability
  • Experiment bookmarking
  • User profiles and preferences
  • Enhanced PDF conversion with more customization

[1.2.0] - Planned (Q2 2026)

  • Fine-tuned embedding model (BioBERT/SciBERT)
  • Multi-language support
  • Real-time collaboration features
  • Integration with external databases (PubMed, UniProt)
  • Advanced analytics dashboard

[2.0.0] - Planned (Q3 2026)

  • Multi-tenancy support
  • GraphQL API
  • WebSocket support for real-time updates
  • Machine learning recommendations
  • Mobile application

Contributing

See CONTRIBUTING.md for guidelines on how to contribute to this project.

Support

For questions, issues, or feature requests, please open an issue on GitHub or contact us at support@biohub.example.com.
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