| # Changelog | |
| All notable changes to Cancer@Home v2 will be documented in this file. | |
| ## [2.0.0] - 2025-11-19 | |
| ### 🎉 Initial Release | |
| #### Added | |
| - **Core Infrastructure** | |
| - FastAPI backend with REST and GraphQL APIs | |
| - Neo4j graph database integration | |
| - Docker Compose setup for easy deployment | |
| - Python virtual environment configuration | |
| - Comprehensive YAML-based configuration system | |
| - **BOINC Integration** | |
| - Distributed computing task submission | |
| - Task status monitoring and tracking | |
| - Support for variant calling, BLAST, and alignment tasks | |
| - Task statistics and performance metrics | |
| - JSON-based task persistence | |
| - **GDC Data Portal Integration** | |
| - API client for GDC cancer data | |
| - File search and download capabilities | |
| - Support for TCGA and TARGET projects | |
| - MAF and VCF file parsers | |
| - Clinical data extraction | |
| - **Bioinformatics Pipeline** | |
| - FASTQ quality control and filtering | |
| - Adapter trimming | |
| - BLAST sequence alignment (BLASTN/BLASTP) | |
| - Variant calling from sequencing data | |
| - Cancer variant identification | |
| - Tumor mutation burden calculation | |
| - **Neo4j Graph Database** | |
| - Comprehensive graph schema (Genes, Mutations, Patients, Cancer Types) | |
| - Repository pattern for data access | |
| - GraphQL schema with flexible querying | |
| - Sample dataset with 7 genes, 5 mutations, 5 patients, 4 cancer types | |
| - Optimized with constraints and indexes | |
| - **Web Dashboard** | |
| - Modern, responsive HTML5/CSS3/JavaScript interface | |
| - 5 main sections: Dashboard, Neo4j Visualization, BOINC Tasks, GDC Data, Pipeline | |
| - Interactive D3.js graph visualization | |
| - Chart.js analytics and statistics | |
| - Real-time data updates | |
| - Clean gradient-based design | |
| - **API Endpoints** | |
| - `/api/health` - System health check | |
| - `/api/neo4j/summary` - Database statistics | |
| - `/api/neo4j/genes/{symbol}` - Gene information | |
| - `/api/boinc/*` - BOINC task management | |
| - `/api/gdc/*` - GDC data access | |
| - `/api/pipeline/*` - Bioinformatics tools | |
| - `/graphql` - GraphQL playground | |
| - `/docs` - Swagger API documentation | |
| - **Documentation** | |
| - Comprehensive README with installation guide | |
| - Quick start guide (QUICKSTART.md) | |
| - Detailed user guide (USER_GUIDE.md) | |
| - GraphQL query examples (GRAPHQL_EXAMPLES.md) | |
| - Architecture documentation (ARCHITECTURE.md) | |
| - Project summary (PROJECT_SUMMARY.md) | |
| - MIT License | |
| - **Setup & Deployment** | |
| - Automated Windows setup script (setup.ps1) | |
| - Automated Linux/Mac setup script (setup.sh) | |
| - One-command application launcher (run.py) | |
| - Rich terminal output with progress tracking | |
| - Automatic directory structure creation | |
| - Database schema initialization | |
| - **Testing** | |
| - Comprehensive test suite (test_cancer_at_home.py) | |
| - Module import tests | |
| - Integration tests | |
| - Directory structure validation | |
| #### Features Highlights | |
| ✓ **Easy Installation**: 5-minute setup with automated scripts | |
| ✓ **Interactive Dashboard**: Modern web UI with real-time updates | |
| ✓ **Graph Visualization**: Neo4j-powered relationship mapping | |
| ✓ **Flexible Querying**: Both REST and GraphQL APIs | |
| ✓ **Distributed Computing**: BOINC integration for heavy workloads | |
| ✓ **Real Data**: GDC Portal integration for cancer genomics | |
| ✓ **Bioinformatics**: Complete FASTQ → BLAST → VCF pipeline | |
| ✓ **Well Documented**: 7 documentation files covering all aspects | |
| ✓ **Production Ready**: Error handling, logging, configuration | |
| #### Technical Specifications | |
| - **Python**: 3.8+ | |
| - **Neo4j**: 5.13 Community Edition | |
| - **FastAPI**: 0.104.1 | |
| - **Docker**: Latest | |
| - **Supported OS**: Windows, Linux, macOS | |
| #### Sample Data Included | |
| **Genes**: TP53, BRAF, BRCA1, BRCA2, PIK3CA, KRAS, EGFR | |
| **Cancer Types**: Breast Cancer, Lung Adenocarcinoma, Colon Adenocarcinoma, Glioblastoma | |
| **Projects**: TCGA-BRCA, TCGA-LUAD, TCGA-COAD, TCGA-GBM, TARGET-AML | |
| --- | |
| ## Version Numbering | |
| This project follows [Semantic Versioning](https://semver.org/): | |
| - **MAJOR**: Incompatible API changes | |
| - **MINOR**: New functionality, backwards compatible | |
| - **PATCH**: Bug fixes, backwards compatible | |
| --- | |
| ## Future Roadmap | |
| ### Planned Features (v2.1.0) | |
| - [ ] Machine learning for mutation prediction | |
| - [ ] Multi-omics data integration (RNA-seq, proteomics) | |
| - [ ] Advanced graph algorithms (PageRank, community detection) | |
| - [ ] Export and report generation (PDF, Excel) | |
| - [ ] User authentication and authorization | |
| - [ ] Data caching for improved performance | |
| ### Planned Features (v2.2.0) | |
| - [ ] Survival analysis and clinical outcomes | |
| - [ ] Drug response prediction | |
| - [ ] Mobile-responsive design improvements | |
| - [ ] Real-time collaboration features | |
| - [ ] Batch data import wizard | |
| - [ ] Advanced search and filtering | |
| ### Long-term Goals | |
| - [ ] Cloud deployment support (AWS, Azure, GCP) | |
| - [ ] Kubernetes orchestration | |
| - [ ] Microservices architecture | |
| - [ ] Real-time BOINC cluster management | |
| - [ ] Integration with additional data sources | |
| - [ ] AI-powered data analysis | |
| --- | |
| ## Contributing | |
| Contributions are welcome! Please see CONTRIBUTING.md (to be created) for guidelines. | |
| --- | |
| ## Support | |
| For issues, questions, or suggestions: | |
| - Check the documentation first | |
| - Review logs in `logs/cancer_at_home.log` | |
| - Open a GitHub issue (if applicable) | |
| --- | |
| ## Acknowledgments | |
| Built with inspiration from: | |
| - Cancer@Home v1 (HeroX DCx Challenge) | |
| - Andrew Kamal's Neo4j Cancer Visualization Dashboard | |
| - The Cancer Genome Atlas (TCGA) Project | |
| - BOINC Project at UC Berkeley | |
| Data provided by: | |
| - Genomic Data Commons (GDC) Portal | |
| - National Cancer Institute (NCI) | |
| - The Cancer Genome Atlas Program | |
| --- | |
| **Cancer@Home v2** - Making cancer genomics research accessible, distributed, and visual. | |