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Initial commit: Add serojump web application with GitHub Pages deployment
- Interactive web widget for serojump with Bayesian inference - Upload CSV data or generate simulated trajectories - MCMC fitting with convergence diagnostics - Performance optimizations for large step counts - Responsive design with serojump logo - GitHub Actions workflow for automatic deployment
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‎.github/workflows/deploy.yml‎

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name: Deploy to GitHub Pages
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on:
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push:
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branches: [ main, master ]
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pull_request:
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branches: [ main, master ]
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permissions:
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contents: read
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pages: write
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id-token: write
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concurrency:
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group: "pages"
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cancel-in-progress: false
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jobs:
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build:
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runs-on: ubuntu-latest
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steps:
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- name: Checkout
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uses: actions/checkout@v4
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- name: Setup Pages
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uses: actions/configure-pages@v4
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- name: Upload artifact
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uses: actions/upload-pages-artifact@v3
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with:
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path: './web'
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deploy:
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environment:
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name: github-pages
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url: ${{ steps.deployment.outputs.page_url }}
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runs-on: ubuntu-latest
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needs: build
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steps:
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- name: Deploy to GitHub Pages
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id: deployment
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uses: actions/deploy-pages@v4

‎.gitignore‎

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# Build artifacts
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build/
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*.o
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*.so
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*.dylib
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*.dll
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*.exe
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# IDE files
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.vscode/
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.idea/
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*.swp
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*.swo
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*~
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# OS files
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.DS_Store
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Thumbs.db
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# Temporary files
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*.tmp
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*.temp
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Untitled-*
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# Logs
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*.log
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# Node modules (if any)
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node_modules/
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# Python cache (if any)
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__pycache__/
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*.pyc
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*.pyo

‎CMakeLists.txt‎

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# CMakeLists.txt - SeroJump WebAssembly Widget (C++ + WebAssembly)
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cmake_minimum_required(VERSION 3.10)
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project(SeroJumpWASM)
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set(CMAKE_CXX_STANDARD 17)
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set(CMAKE_CXX_STANDARD_REQUIRED ON)
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# Source directory
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set(SOURCE_DIR "${CMAKE_CURRENT_SOURCE_DIR}/src")
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# Check if we're building with Emscripten (for WASM) or native (for server)
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if(EMSCRIPTEN)
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message(STATUS "🧬 Building SeroJump WebAssembly module with Emscripten")
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# WebAssembly module
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add_executable(serojump_module "${SOURCE_DIR}/serojump.cpp")
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# Enable embind for this target
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set(CMAKE_EXE_LINKER_FLAGS "${CMAKE_EXE_LINKER_FLAGS} --bind")
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# Set output directory
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set_target_properties(serojump_module PROPERTIES
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RUNTIME_OUTPUT_DIRECTORY "${CMAKE_BINARY_DIR}/web"
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)
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# Set Emscripten link flags for serojump
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set_target_properties(serojump_module PROPERTIES
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LINK_FLAGS "-s WASM=1 \
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-s 'EXPORTED_RUNTIME_METHODS=[\"ccall\",\"cwrap\"]' \
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-s 'EXPORTED_FUNCTIONS=[\"_malloc\",\"_free\"]' \
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-s ALLOW_MEMORY_GROWTH=1 \
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-s NO_EXIT_RUNTIME=1 \
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-s MODULARIZE=1 \
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-s 'EXPORT_NAME=\"createSeroJumpModule\"' \
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-s STACK_SIZE=1MB \
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-s TOTAL_MEMORY=64MB \
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--no-entry"
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)
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# Include headers
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target_include_directories(serojump_module PRIVATE "${SOURCE_DIR}")
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else()
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message(STATUS "🚀 Building native C++ HTTP server for SeroJump")
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# Find required packages for the server
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find_package(Threads REQUIRED)
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# C++ HTTP Server (reuse existing server.cpp from sir_bayes)
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add_executable(serojump_server "${SOURCE_DIR}/server.cpp")
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# Link threads library
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target_link_libraries(serojump_server PRIVATE Threads::Threads)
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# Set output directory
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set_target_properties(serojump_server PROPERTIES
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RUNTIME_OUTPUT_DIRECTORY "${CMAKE_BINARY_DIR}"
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)
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# Enable filesystem library support
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if(CMAKE_CXX_COMPILER_ID STREQUAL "GNU" AND CMAKE_CXX_COMPILER_VERSION VERSION_LESS "9.0")
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target_link_libraries(serojump_server PRIVATE stdc++fs)
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endif()
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endif()
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# Custom target to build both WASM and server
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add_custom_target(build_all
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COMMENT "Building both SeroJump WebAssembly module and C++ server"
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)
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‎DEPLOYMENT.md‎

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# GitHub Pages Deployment
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This repository is set up for automatic deployment to GitHub Pages using GitHub Actions.
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## Setup Instructions
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1. **Push your code to GitHub**:
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```bash
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git add .
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git commit -m "Add GitHub Pages deployment"
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git push origin main
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```
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2. **Enable GitHub Pages in your repository**:
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- Go to your repository on GitHub
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- Click on "Settings" tab
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- Scroll down to "Pages" section
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- Under "Source", select "GitHub Actions"
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- The workflow will automatically deploy from the `web/` directory
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3. **Access your site**:
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- Your site will be available at: `https://[your-username].github.io/[repository-name]`
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- For example: `https://davidhodgson.github.io/serojump`
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## How it works
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- The GitHub Actions workflow (`.github/workflows/deploy.yml`) automatically runs on every push to the main branch
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- It deploys the contents of the `web/` directory to GitHub Pages
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- No build step is required since this is a static HTML/JS/CSS site
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## File Structure
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```
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serojump/
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├── .github/
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│ └── workflows/
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│ └── deploy.yml # GitHub Actions workflow
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├── web/
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│ ├── index.html # Main page
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│ ├── serojump-app.js # Application logic
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│ ├── serojump_module.js # WebAssembly module
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│ ├── serojump_hex.png # Logo
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│ └── sample_data.csv # Sample data
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└── DEPLOYMENT.md # This file
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```
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## Troubleshooting
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- If deployment fails, check the "Actions" tab in your GitHub repository
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- Make sure the `web/` directory contains all necessary files
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- Ensure your repository is public (required for free GitHub Pages)

‎README.md‎

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# SeroJump WebAssembly Widget
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Interactive web application for simulating individual antibody trajectories and fitting them using serojump-style reversible-jump MCMC.
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## Features
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- **Individual Trajectory Simulation**: Simulate 10 individuals with mixed infection histories
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- **Antibody Kinetics**: Model IgG titre dynamics with infection events
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- **Real-time RJ-MCMC**: Bayesian inference for infection probabilities
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- **Interactive Visualization**: Real-time parameter traces and trajectory plots
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- **WebAssembly Performance**: High-speed C++ core compiled to WASM
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## Architecture
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### Data Model
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```cpp
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struct Individual {
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int id;
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vector<double> sample_times; // when samples were taken
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vector<double> titre_values; // observed IgG titres
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vector<double> infection_times; // true infection times (for simulation)
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double infection_prob; // fitted infection probability
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};
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```
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### Antibody Kinetics
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- **Pre-infection**: Baseline titre with noise
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- **Post-infection**: Exponential rise then decay
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- **Function**: `titre = baseline + boost * exp(-decay * (t - t_inf))` for t > t_inf
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### RJ-MCMC Components
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1. **Parameter updates**: baseline titre, boost, decay, noise
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2. **Infection time updates**: continuous time proposals
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3. **Model selection**: infected vs uninfected states
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4. **Acceptance criteria**: Metropolis-Hastings with jacobians
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## Quick Start
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```bash
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./build.sh
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./start.sh
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```
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Visit http://localhost:2020 to use the widget.

‎build.sh‎

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#!/bin/bash
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# Colors for output
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RED='\033[0;31m'
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GREEN='\033[0;32m'
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YELLOW='\033[1;33m'
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BLUE='\033[0;34m'
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NC='\033[0m' # No Color
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echo -e "${BLUE}🧬 SeroJump WebAssembly Build Script${NC}"
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echo "======================================"
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# Check if build directory exists
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if [ ! -d "build" ]; then
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echo -e "${YELLOW}📁 Creating build directory...${NC}"
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mkdir -p build
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fi
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# Build native server first
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echo -e "${BLUE}🚀 Building native C++ server...${NC}"
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cd build
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cmake .. -DCMAKE_BUILD_TYPE=Release
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if make serojump_server; then
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echo -e "${GREEN}✅ Native server built successfully!${NC}"
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else
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echo -e "${RED}❌ Failed to build native server${NC}"
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exit 1
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fi
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cd ..
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# Check if emsdk is available
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if command -v emcc &> /dev/null; then
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echo -e "${BLUE}🌊 Building WebAssembly module...${NC}"
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# Create web output directory
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mkdir -p build/web
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# Build with Emscripten
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cd build
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emcmake cmake .. -DCMAKE_BUILD_TYPE=Release
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if emmake make serojump_module; then
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echo -e "${GREEN}✅ WebAssembly module built successfully!${NC}"
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# Copy the generated files to web directory
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if [ -f "web/serojump_module.js" ] && [ -f "web/serojump_module.wasm" ]; then
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echo -e "${GREEN}📦 WebAssembly files generated:${NC}"
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echo " - serojump_module.js"
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echo " - serojump_module.wasm"
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else
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echo -e "${YELLOW}⚠️ Warning: Expected WASM files not found in web directory${NC}"
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fi
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else
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echo -e "${RED}❌ Failed to build WebAssembly module${NC}"
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exit 1
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fi
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cd ..
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else
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echo -e "${YELLOW}⚠️ Warning: Emscripten not found. Skipping WebAssembly build.${NC}"
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echo "To install Emscripten:"
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echo "1. Clone emsdk: git clone https://github.com/emscripten-core/emsdk.git"
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echo "2. Run: ./emsdk/emsdk install latest && ./emsdk/emsdk activate latest"
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echo "3. Source: source ./emsdk/emsdk_env.sh"
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fi
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echo ""
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echo -e "${GREEN}🎉 Build completed!${NC}"
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if [ -f "build/serojump_server" ]; then
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echo -e "${BLUE}▶️ To start the server: ./start.sh${NC}"
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else
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echo -e "${RED}❌ Server binary not found${NC}"
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fi
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