QUICKSTART.md

Quick Start Guide

Prerequisites

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

Installation

Windows

# Run in PowerShell as Administrator
.\setup.ps1

Linux/Mac

chmod +x setup.sh
./setup.sh

Manual Installation

1. Create virtual environment

python -m venv venv

# Windows
venv\Scripts\activate

# Linux/Mac
source venv/bin/activate

2. Install dependencies

pip install -r requirements.txt

3. Start Neo4j

docker-compose up -d

4. Run application

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:

# 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

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

curl http://localhost:5000/api/neo4j/summary

Search GDC Files

curl http://localhost:5000/api/gdc/files/TCGA-BRCA?limit=10

Troubleshooting

Docker not starting

# 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

# 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

pytest

Format code

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