QUICKSTART.md

# Quick Start Guide

## Prerequisites
- Python 3.8 or higher
- Docker Desktop
- 8GB RAM minimum (16GB recommended)
- Windows, macOS, or Linux

## Installation

### Windows
```powershell
# Run in PowerShell as Administrator
.\setup.ps1
```

### Linux/Mac
```bash
chmod +x setup.sh
./setup.sh
```

## Manual Installation

1. **Create virtual environment**
```bash
python -m venv venv

# Windows
venv\Scripts\activate

# Linux/Mac
source venv/bin/activate
```

2. **Install dependencies**
```bash
pip install -r requirements.txt
```

3. **Start Neo4j**
```bash
docker-compose up -d
```

4. **Run application**
```bash
python run.py
```

## First Time Usage

1. Open browser to http://localhost:5000
2. The database will auto-initialize with sample data
3. Explore the dashboard tabs:
   - **Dashboard**: Overview statistics
   - **Neo4j Visualization**: Interactive graph
   - **BOINC Tasks**: Distributed computing
   - **GDC Data**: Cancer genomics data
   - **Analysis Pipeline**: Bioinformatics tools

## GraphQL Queries

Access GraphQL playground at: http://localhost:5000/graphql

Example queries:

```graphql
# Get all genes
query {
  genes(limit: 10) {
    symbol
    name
    chromosome
  }
}

# Get mutations for a gene
query {
  mutations(gene: "TP53") {
    chromosome
    position
    consequence
  }
}

# Get patients with cancer type
query {
  patients(project_id: "TCGA-BRCA") {
    patient_id
    age
    gender
  }
}
```

## API Examples

### Submit BOINC Task
```bash
curl -X POST http://localhost:5000/api/boinc/submit \
  -H "Content-Type: application/json" \
  -d '{"workunit_type": "variant_calling", "input_file": "sample.fastq"}'
```

### Get Database Summary
```bash
curl http://localhost:5000/api/neo4j/summary
```

### Search GDC Files
```bash
curl http://localhost:5000/api/gdc/files/TCGA-BRCA?limit=10
```

## Troubleshooting

### Docker not starting
```bash
# Check Docker status
docker ps

# Restart Docker containers
docker-compose down
docker-compose up -d
```

### Neo4j connection error
1. Wait 30 seconds for Neo4j to fully start
2. Check Neo4j Browser: http://localhost:7474
3. Login: username=neo4j, password=cancer123

### Python module errors
```bash
# Reinstall dependencies
pip install --upgrade -r requirements.txt
```

## Configuration

Edit `config.yml` to customize:
- Neo4j connection
- GDC API settings
- BOINC configuration
- Pipeline parameters

## Data Sources

### GDC Portal Projects
- TCGA-BRCA: Breast Cancer
- TCGA-LUAD: Lung Adenocarcinoma
- TCGA-COAD: Colon Adenocarcinoma
- TCGA-GBM: Glioblastoma
- TARGET-AML: Acute Myeloid Leukemia

### Sample Data
The system includes sample data for demonstration:
- 7 cancer-associated genes (TP53, BRAF, BRCA1, BRCA2, etc.)
- 5 mutation records
- 5 patient cases
- 4 cancer types

## Development

### Run tests
```bash
pytest
```

### Format code
```bash
black backend/
```

### API Documentation
http://localhost:5000/docs (Swagger UI)

## Support

For issues or questions:
- Check logs: `logs/cancer_at_home.log`
- Review configuration: `config.yml`
- Consult README.md for detailed information