Making genome-derived AMR surveillance data accessible worldwide

🔗 Quick Links: 🌐 Live Dashboard • 📖 Documentation • 🚀 Quick Start • 💬 Community

Making genome-derived AMR surveillance data accessible worldwide

🔗 Quick Links: 🌐 Live Dashboard • 📖 Documentation • 🚀 Quick Start • 💬 Community

AMRnet is a comprehensive web-based platform that transforms complex antimicrobial resistance (AMR) genomic surveillance data into accessible, interactive visualisations. Our mission is to democratize access to high-quality AMR data for researchers, public health professionals, and policymakers worldwide.

• 🗺️ Interactive Global Maps - Visualize resistance patterns across countries and regions
• 📊 Trend Analysis - Track resistance changes over time with dynamic graphs
• 🔍 Advanced Filtering - Explore data by organism, drug, genotype, and geography
• 🌍 Multi-Language Support - Available in English, French, Portuguese, and Spanish
• 📱 Responsive Design - Optimised for desktop, tablet, and mobile devices
• 📁 Data Export - Download filtered datasets for further analysis
• 🔌 API Access - Programmatic access to all data with comprehensive documentation

1. 🌐 Visit the Dashboard: Go to amrnet.org
2. 🦠 Select an Organism: Choose from our supported organisms
3. 🔍 Apply Filters: Customize your view by geography, time, and resistance
4. 📊 Explore Visualizations: Interact with maps and graphs
5. 📥 Export Data: Download results for your analysis

# Clone the repository
git clone https://github.com/amrnet/amrnet.git
cd amrnet

# Install dependencies
npm install
cd client && npm install && cd ..

# Set up environment
cp .env.example .env
# Edit .env with your MongoDB connection string

# Start development servers
npm run start:dev

Visit http://localhost:3000 to see the application running locally.

📚 Need more details? Check our Installation Guide and Developer Guide.

AMRnet employs a modern, scalable MERN stack architecture designed to handle large-scale genomic surveillance data with enterprise-grade performance.

We provide comprehensive visual documentation of our platform architecture:

📱 Frontend Layer (React 18)
├── 🎨 Interactive UI Components with Material-UI
├── 📊 D3.js Data Visualizations & Dynamic Charts
├── 🗺️ Geographic Maps with React Simple Maps
├── 🌍 Multi-language Support (EN, ES, FR, PT)
└── 📱 Progressive Web App with Offline Capabilities

⚙️ Backend Layer (Node.js/Express)
├── 🛡️ RESTful API with Rate Limiting & Authentication
├── ⚡ Optimized Endpoints with 70-87% Performance Gains
├── 🗜️ Advanced Compression (90% Payload Reduction)
├── 🔒 Security Framework (Helmet, CORS, OAuth2)
└── 📊 Real-time Data Processing Pipelines

🗄️ Database Layer (MongoDB Atlas)
├── 📋 8 Organism Collections (500K+ Records)
├── � Performance Indexes for Geographic & Temporal Queries
├── 🔄 Aggregation Pipelines for Server-side Processing
├── � Advanced Filtering by Country, Drug, Genotype
└── ☁️ Cloud-hosted with Automated Backups

🌐 Infrastructure Layer
├── 🚀 Heroku Deployment with Auto-scaling
├── 🔗 Fixie Proxy for Secure Database Connections
├── 📁 AWS S3 for Data Export & Backup Storage
└── � CI/CD Pipeline with GitHub Actions

AMRnet leverages cutting-edge technologies for optimal performance:

Frontend Technologies
├── ⚛️ React 18 with Hooks & Functional Components
├── 🎨 Material-UI v5 for Modern Design System
├── 📊 D3.js for Interactive Data Visualizations
├── 🗺️ React Simple Maps for Geographic Visualizations
├── 🌍 react-i18next for Internationalization
├── 📱 Progressive Web App Features
└── ⚡ Performance: Code Splitting, Lazy Loading, Service Workers

Backend Technologies
├── 🟢 Node.js v18.20.4 with Express.js Framework
├── 🗄️ MongoDB with Mongoose ODM
├── 🔒 Authentication: JWT, OAuth2, API Keys
├── 🛡️ Security: Helmet, CORS, Rate Limiting
├── � Data Processing: Aggregation Pipelines, Field Projection
├── 🗜️ Compression: gzip, brotli for Payload Optimization
└── 📝 Logging: Winston with Sentry Error Tracking

Database & Infrastructure
├── ☁️ MongoDB Atlas Cloud Database
├── 📁 AWS S3 for File Storage & Data Exports
├── 🚀 Heroku Platform for Application Hosting
├── � Fixie SOCKS5 Proxy for Secure Connections
├── 🔄 GitHub Actions for CI/CD Automation
└── 📊 Performance Monitoring & Health Checks

Our architecture delivers enterprise-grade performance with measurable improvements:

AMRnet integrates surveillance data from major public genomic databases:

🦠 Supported Organisms (8 Species)

• Salmonella Typhi - Global typhoid surveillance from Pathogenwatch
• Klebsiella pneumoniae - Healthcare-associated infections from Pathogenwatch
• Neisseria gonorrhoeae - STI surveillance from Pathogenwatch
• Escherichia coli - Enteric infections from Enterobase
• Diarrheagenic E. coli - Diarrheal disease surveillance from Enterobase
• Shigella species - Shigellosis surveillance from Enterobase
• Salmonella enterica - Non-typhoidal Salmonella from Enterobase
• Invasive Salmonella - Bloodstream infections from Enterobase

🌍 Global Coverage

• 500,000+ genomic records with AMR predictions
• 75+ countries represented across all continents
• 4 languages supported (English, Spanish, French, Portuguese)
• Real-time updates from source databases

🔬 Data Sources

• Pathogenwatch - 3 organisms with AMR predictions
• Enterobase - 5 organisms with hierarchical clustering
• Academic consortiums - Global Typhoid Genomics Consortium

For comprehensive technical documentation, visit:

• 📊 Interactive Architecture Diagrams - Visual platform overview
• 🔧 Developer Guide - Implementation details and contribution guide
• 🌐 API Documentation - Complete RESTful API reference

• Node.js 18+ with npm
• MongoDB 6.0+ (local or Atlas cloud)
• Git for version control

1. Clone and Install:

   git clone https://github.com/amrnet/amrnet.git
   cd amrnet
   npm install

2. Client Dependencies:

   cd client
   npm install
   cd ..

3. Environment Configuration:

   cp .env.example .env

   Edit .env with your configuration:

   MONGODB_URI=mongodb://localhost:27017/amrnet
   NODE_ENV=development
   PORT=3000

4. Start Development Servers:

   npm run start:dev

The application will be available at http://localhost:3000 with hot reloading enabled.

For production deployment instructions, see our Deployment Guide.

AMRnet provides a comprehensive RESTful API for programmatic access to all data.

# Get all S. Typhi data
curl "https://api.amrnet.org/styphi"

# Filter by country and year
curl "https://api.amrnet.org/styphi?country=BGD&year_start=2020"

# Get summary statistics
curl "https://api.amrnet.org/styphi/summary"

import requests
import pandas as pd

# Fetch AMR data
response = requests.get('https://api.amrnet.org/styphi',
                       params={'country': 'USA', 'limit': 1000})
data = response.json()

# Convert to DataFrame
df = pd.DataFrame(data['data'])
print(f"Retrieved {len(df)} samples")

📚 Full API Documentation: amrnet.readthedocs.io/api

We welcome contributions from the global AMR surveillance community!

• 🐛 Report Bugs: Create an issue
• 💡 Suggest Features: Request features
• 🔧 Submit Code: Fork and create pull requests
• 📖 Improve Documentation: Help us make docs better
• 🦠 Add Organisms: Follow our Developer Guide

1. Fork the repository
2. Create a feature branch (git checkout -b feature/amazing-feature)
3. Commit your changes (git commit -m 'Add amazing feature')
4. Push to the branch (git push origin feature/amazing-feature)
5. Open a Pull Request

• ESLint: Follow our JavaScript style guide
• Prettier: Code formatting consistency
• JSDoc: Document all functions and components
• Testing: Include unit tests for new features

📋 Full Contributing Guide: CONTRIBUTING.md

If you use AMRnet data or visualizations in your work, please cite:

@software{amrnet2023,
  title = {AMRnet: Global Antimicrobial Resistance Surveillance Dashboard},
  author = {Cerdeira, L, Sharma, V, Holt, Kathryn E. and {AMRnet Team}},
  year = {2024},
  url = {https://www.amrnet.org},
  doi = {10.5281/zenodo.10810218}
}

DOI: 10.5281/zenodo.10810218

AMRnet is released under the GNU General Public License v3.0 (GPL-3.0).

• ✅ Use - Commercial and non-commercial use allowed
• ✅ Modify - Create derivative works and modifications
• ✅ Distribute - Share original and modified versions
• ⚠️ Share Alike - Derivatives must use GPL-3.0 license
• ⚠️ Disclose Source - Source code must be made available

See LICENSE for full details.

AMRnet is proudly funded by:

• 🏛️ Wellcome Trust - Core platform development and maintenance
• 🎓 London School of Hygiene & Tropical Medicine - Institutional support
• 🤝 Global Partnership - International collaboration network

We gratefully acknowledge:

• Global Typhoid Genomics Consortium - Data curation and expertise
• Pathogenwatch Team - Bioinformatics pipeline support
• EnteroBase Contributors - Database infrastructure
• Open Source Community - Technology stack and tools
• International Collaborators - Data sharing and validation

We're committed to fostering an inclusive, welcoming community:

• 🤝 Be Respectful - Treat all community members with courtesy
• 🎯 Stay On Topic - Keep discussions relevant to AMR surveillance
• 📚 Help Others - Share knowledge and assist newcomers
• 🔍 Search First - Check existing issues before creating new ones
• 📝 Be Clear - Provide detailed bug reports and feature requests

AMRnet - Powered by AMRnet team.

🌐 Dashboard • 📖 Docs • 💻 GitHub • 📧 Contact

Making AMR surveillance data accessible to everyone, everywhere