A comprehensive, interactive short course designed to teach version control fundamentals and infectious disease modeling using the powerful odin and monty packages. This course is structured for maximum learning in minimal time with hands-on, collaborative learning experiences.
Duration: 8 hours total (4 hours per part)
Format: Interactive online learning with real-time collaboration
Target Audience: Students, researchers, and professionals in public health and computational modeling
- Module 1: Introduction to Version Control
- Module 2: GitHub Collaboration
- Module 3: R with Git & GitHub
- Module 4: Introduction to odin
- Module 5: Model Fitting with monty
- Module 6: Advanced Applications
- Live Code Execution: Run Git commands and R code directly in the browser
- Real-time Collaboration: Work with classmates in real-time
- Progress Tracking: Monitor your learning progress
- Instant Feedback: Get immediate results from your code
- Git Terminal Simulator: Practice Git commands with realistic responses
- R Studio Environment: Execute odin & monty code in a familiar interface
- Model Building: Create and simulate infectious disease models
- Parameter Exploration: Experiment with different model parameters
- Live Chat: Discuss problems and solutions with peers
- Status Sharing: See what classmates are working on
- Group Discussions: Learn from collective experiences
- Peer Support: Help and get help from fellow students
- Frontend: Modern HTML5, CSS3, JavaScript (ES6+)
- Interactive Elements: Custom terminal simulator, R Studio interface
- Real-time Features: WebSocket-like collaboration system
- Responsive Design: Works on all devices and screen sizes
- Progressive Web App: Installable, offline-capable web application
- Dark Mode: Automatic theme switching with system preference detection
- Error Handling: Comprehensive error tracking and user-friendly notifications
- Performance Monitoring: Real-time performance and memory usage tracking
- Git Fundamentals: Industry best practices for version control
- Odin-Monty Workshop: Materials from Imperial College London MRC-IDE team
- Real-world Applications: Practical examples from infectious disease research
- Git Command Simulator: Practice version control commands
- R Code Executor: Run epidemiological models
- Collaboration Platform: Real-time peer interaction
- Progress Dashboard: Track your learning journey
- Basic computer literacy
- Interest in version control and/or infectious disease modeling
- No prior Git or R experience required
- Git: Download from git-scm.com
- R: Download from cran.r-project.org (4.4.x recommended)
- RStudio: Download from posit.co
- Install as App: Click the install button to add to your home screen
- Offline Access: Course content works without internet connection
- Push Notifications: Get notified about course updates and new content
- Background Sync: Automatically sync your progress when online
# Install required packages from R-universe
install.packages(
c("monty", "dust2", "odin2"),
repos = c("https://mrc-ide.r-universe.dev", "https://cloud.r-project.org")
)By the end of this course, you will be able to:
- ✅ Use Git for tracking changes in your projects
- ✅ Collaborate effectively on GitHub
- ✅ Manage R projects with version control
- ✅ Implement reproducible research practices
- ✅ Build epidemiological models with odin
- ✅ Fit models to data using monty
- ✅ Interpret model outputs and parameters
- ✅ Apply models to real-world scenarios
- Practice Git commands with realistic responses
- Learn through trial and error
- Get instant feedback on your commands
- Build confidence with version control
- Familiar R Studio-like environment
- Execute odin & monty code
- View model outputs and plots
- Experiment with parameters
- See classmates' progress in real-time
- Chat and discuss problems
- Share solutions and insights
- Build a learning community
- Dark/Light Mode: Toggle between themes or follow system preference
- Offline Mode: Continue learning without internet connection
- Install as App: Add to home screen for app-like experience
- Smart Notifications: Get helpful reminders and course updates
- Performance Monitoring: Automatic detection of performance issues
- Error Recovery: Graceful error handling with helpful suggestions
The course platform is optimized for all devices:
- Desktop: Full-featured experience with side-by-side collaboration
- Tablet: Touch-friendly interface with adaptive layouts
- Mobile: Streamlined mobile experience for on-the-go learning
- Modern Browsers: Chrome 90+, Firefox 88+, Safari 14+, Edge 90+
- Mobile Browsers: iOS Safari 14+, Chrome Mobile 90+
- Progressive Enhancement: Core functionality works without JavaScript
This course is designed to be deployed on GitHub Pages:
- Push to GitHub: Upload your course materials
- Enable Pages: Configure GitHub Pages in repository settings
- Custom Domain: Optionally configure a custom domain
- HTTPS: Automatic SSL certificate from GitHub
The course automatically becomes a PWA when deployed:
- Service Worker: Automatically caches content for offline use
- Manifest: Provides app-like installation experience
- Offline Support: Core functionality works without internet
- Push Notifications: Ready for future notification features
For local development and testing:
# Clone the repository
git clone https://github.com/yourusername/g-wac-course.git
# Open in your browser
# Or use a local server
python -m http.server 8000
# Then visit http://localhost:8000- Error Tracking: Comprehensive error logging and debugging tools
- Performance Monitoring: Real-time performance metrics
- Theme Development: Easy theme customization with CSS variables
- PWA Testing: Test PWA features in development mode
We welcome contributions to improve the course:
- Fork the repository
- Create a feature branch
- Make your improvements
- Submit a pull request
- Additional interactive exercises
- More model examples
- Improved collaboration features
- Accessibility enhancements
- Translation to other languages
This course is based on materials from the Odin-Monty Workshop and is released under appropriate licenses for educational use.
- Imperial College London MRC-IDE Team: For the excellent odin-monty workshop materials
- G-WAC Community: For supporting this educational initiative
- Open Source Community: For the tools and frameworks that make this possible
- Course Issues: Check existing issues or create new ones
- Technical Problems: Contact the development team
- Content Questions: Reach out to course instructors
- Course Updates: Follow the repository for new features
- Community: Join G-WAC discussions and events
- Feedback: Share your experience and suggestions
- Install Software: Git, R, and RStudio
- Join Course: Access the course platform
- Start Learning: Begin with Part 1 (Git & GitHub)
- Practice: Use interactive features to reinforce learning
- Collaborate: Work with classmates in real-time
- Build Models: Create infectious disease models in Part 2
- Apply Knowledge: Use skills in your own projects
Built with ❤️ for the G-WAC community
Empowering the next generation of computational modelers