OpenPeerAI/CancerAtHomeV2

Cancer@Home v2

A distributed computing platform for cancer genomics research, combining BOINC distributed computing, GDC cancer data analysis, sequence processing (FASTQ/BLAST), and Neo4j graph visualization.

🚀 Quick Start (5 minutes)

Prerequisites

• Python 3.8+
• Docker Desktop
• 8GB RAM minimum

Installation

1. Clone and setup

cd CancerAtHome2
python -m venv venv
venv\Scripts\activate  # Windows
pip install -r requirements.txt

2. Start Neo4j Database

docker-compose up -d

3. Run the application

python run.py

4. Open your browser

• Application: http://localhost:5000
• Neo4j Browser: http://localhost:7474 (username: neo4j, password: cancer123)

🎯 Features

1. Distributed Computing (BOINC Integration)

• Submit cancer research computational tasks
• Monitor distributed workload processing
• Real-time task status tracking

2. GDC Data Integration

• Download cancer genomics data from GDC Portal
• Support for various cancer types (TCGA, TARGET projects)
• Automatic data parsing and normalization

3. Sequence Analysis Pipeline

• FASTQ file processing
• BLAST sequence alignment
• Variant calling and annotation

4. Neo4j Graph Database

• Graph-based cancer data modeling
• Relationships: Gene → Mutation → Patient → Cancer Type
• Interactive graph visualization

5. GraphQL API

• Query cancer data flexibly
• Filter by gene, mutation, patient cohort
• Aggregate statistics

6. Interactive Dashboard

• Real-time data visualization
• Network graphs for gene interactions
• Mutation frequency charts
• Patient cohort analysis

📊 Architecture

Cancer@Home v2
│
├── Frontend (React + D3.js)
│   ├── Dashboard
│   ├── Neo4j Visualization
│   └── Task Monitor
│
├── Backend (FastAPI)
│   ├── REST API
│   ├── GraphQL Endpoint
│   └── WebSocket (real-time updates)
│
├── Data Layer
│   ├── Neo4j (Graph Database)
│   ├── BOINC Client
│   └── GDC API Client
│
└── Analysis Pipeline
    ├── FASTQ Parser
    ├── BLAST Wrapper
    └── Variant Annotator

🗂️ Project Structure

CancerAtHome2/
├── backend/
│   ├── api/              # FastAPI routes
│   ├── boinc/            # BOINC integration
│   ├── gdc/              # GDC data fetcher
│   ├── neo4j/            # Neo4j database layer
│   ├── pipeline/         # Bioinformatics pipeline
│   └── graphql/          # GraphQL schema
├── frontend/
│   ├── public/
│   └── src/
│       ├── components/   # React components
│       ├── views/        # Page views
│       └── api/          # API client
├── data/                 # Downloaded datasets
├── docker-compose.yml    # Neo4j container
├── requirements.txt      # Python dependencies
└── run.py               # Main entry point

🧬 Data Flow

1. Data Ingestion: Download cancer genomics data from GDC Portal
2. Processing: Run FASTQ/BLAST analysis on distributed BOINC network
3. Storage: Store results in Neo4j graph database
4. Visualization: Query and visualize via web dashboard

🔧 Configuration

Edit config.yml to customize:

• Neo4j connection settings
• GDC API parameters
• BOINC project URL
• Analysis pipeline options

📖 Usage Examples

Query Mutations by Gene

query {
  mutations(gene: "TP53") {
    id
    position
    consequence
    patients {
      cancerType
      stage
    }
  }
}

Submit Analysis Task

from backend.boinc import BOINCClient

client = BOINCClient()
task_id = client.submit_task(
    workunit_type="variant_calling",
    input_file="sample.fastq"
)

🤝 Inspired By

• Cancer@Home v1 - Distributed cancer research
• Neo4j Cancer Visualization - Graph-based cancer data modeling

📄 License

MIT License

🛟 Support

For issues or questions, please open a Huggingface or GitHub issue.