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<body>
<!-- Navigation -->
<nav class="nav">
<div class="nav-content">
<div class="nav-title">🧬 AGR MCP Server</div>
<div class="nav-links">
<a href="#overview">Overview</a>
<a href="#features">Features</a>
<a href="#architecture">Architecture</a>
<a href="#installation">Installation</a>
</div>
</div>
</nav>
<main class="main">
<!-- Hero Section -->
<section class="hero">
<div class="container">
<div class="hero-content">
<div class="hero-badge">JavaScript Implementation</div>
<h1>AGR MCP Server</h1>
<h2>Model Context Protocol interface for genomics research</h2>
</div>
</div>
</section>
<!-- Overview Section -->
<section id="overview" class="section">
<div class="container">
<div class="section-header fade-in">
<h2>Project Overview</h2>
<p>A high-performance JavaScript implementation of the Alliance of Genome Resources MCP server, providing seamless access to genomics data through the Model Context Protocol.</p>
</div>
<div class="stats fade-in">
<div class="stat">
<span class="stat-number">12</span>
<span class="stat-label">MCP Tools</span>
</div>
<div class="stat">
<span class="stat-number">3</span>
<span class="stat-label">Server Variants</span>
</div>
<div class="stat">
<span class="stat-number">100%</span>
<span class="stat-label">Node.js</span>
</div>
</div>
</div>
</section>
<!-- Features Section -->
<section id="features" class="section">
<div class="container">
<div class="section-header fade-in">
<h2>Key Features</h2>
<p>Advanced capabilities for modern genomics research workflows</p>
</div>
<div class="cards fade-in">
<div class="card">
<span class="card-icon">🔍</span>
<h3>Advanced Query Engine</h3>
<p>Sophisticated search capabilities with natural language processing</p>
<ul>
<li>Boolean operators (AND, OR, NOT)</li>
<li>Species-specific filtering</li>
<li>Cross-entity search</li>
<li>Process detection</li>
</ul>
</div>
<div class="card">
<span class="card-icon">⚡</span>
<h3>High-Performance Architecture</h3>
<p>Built for speed and reliability with modern Node.js</p>
<ul>
<li>Intelligent caching (5-10 min TTL)</li>
<li>Connection pooling</li>
<li>Rate limiting (100 req/min)</li>
<li>Exponential backoff retry</li>
</ul>
</div>
<div class="card">
<span class="card-icon">🛠️</span>
<h3>Multiple Interfaces</h3>
<p>Flexible access methods for different use cases</p>
<ul>
<li>MCP server for Claude Desktop</li>
<li>CLI tools for command line</li>
<li>Interactive chat interface</li>
<li>Natural language server</li>
</ul>
</div>
<div class="card">
<span class="card-icon">🧬</span>
<h3>Comprehensive Genomics Tools</h3>
<p>12 specialized MCP tools for research workflows</p>
<ul>
<li>Gene search and information</li>
<li>Disease associations</li>
<li>Expression data analysis</li>
<li>BLAST sequence search</li>
</ul>
</div>
</div>
</div>
</section>
<!-- Architecture Section -->
<section id="architecture" class="section">
<div class="container">
<div class="section-header fade-in">
<h2>System Architecture</h2>
<p>Modern, scalable design built on Node.js and the MCP protocol</p>
</div>
<div class="architecture fade-in">
<div class="arch-grid">
<div class="arch-component">
<h4>🖥️ MCP Client</h4>
<p>Claude Desktop integration</p>
</div>
<div class="arch-component">
<h4>🚀 AGR Server</h4>
<p>Core JavaScript implementation</p>
</div>
<div class="arch-component">
<h4>💾 NodeCache</h4>
<p>Intelligent caching layer</p>
</div>
<div class="arch-component">
<h4>🌐 HTTP Client</h4>
<p>Axios with connection pooling</p>
</div>
<div class="arch-component">
<h4>📊 Monitoring</h4>
<p>Performance tracking</p>
</div>
<div class="arch-component">
<h4>🔬 AGR APIs</h4>
<p>Genomics data sources</p>
</div>
</div>
</div>
<div class="cards fade-in">
<div class="card">
<span class="card-icon">🔧</span>
<h3>Technical Stack</h3>
<ul>
<li>Node.js 18+ runtime</li>
<li>MCP protocol compliance</li>
<li>Axios HTTP client</li>
<li>Pino structured logging</li>
<li>Vitest testing framework</li>
<li>ESLint + Prettier</li>
</ul>
</div>
<div class="card">
<span class="card-icon">📈</span>
<h3>Performance Features</h3>
<ul>
<li>Async I/O operations</li>
<li>Memory-efficient design</li>
<li>Automatic cleanup</li>
<li>Input validation</li>
<li>Error handling</li>
<li>Response optimization</li>
</ul>
</div>
</div>
</div>
</section>
<!-- Installation Section -->
<section id="installation" class="section">
<div class="container">
<div class="section-header fade-in">
<h2>Installation & Usage</h2>
<p>Get started with the AGR MCP server in minutes</p>
</div>
<div class="install-options fade-in">
<div class="install-option">
<h3>
📦 npm Package
<span class="badge">Recommended</span>
</h3>
<div class="code-block" data-language="bash">
<span class="comment"># Install globally from npm</span>
<span class="keyword">npm</span> install -g agr-mcp-server-enhanced
<span class="comment"># Available binaries</span>
agr-mcp-server <span class="comment"># Main MCP server</span>
agr-mcp-natural <span class="comment"># Natural language server</span>
alliance <span class="comment"># CLI interface</span>
agr-chat <span class="comment"># Interactive chat</span>
</div>
</div>
<div class="install-option">
<h3>⚙️ From Source</h3>
<div class="code-block" data-language="bash">
<span class="comment"># Clone and setup</span>
<span class="keyword">git</span> clone https://github.com/nuin/agr-mcp-server-js.git
<span class="keyword">cd</span> agr-mcp-server-js
<span class="keyword">npm</span> run setup
</div>
</div>
</div>
<div class="card fade-in">
<span class="card-icon">🔗</span>
<h3>Claude Desktop Configuration</h3>
<p>Connect the MCP server to Claude Desktop for seamless integration</p>
<h4 style="margin-top: 1.5rem; color: #2980b9;">Option 1: npm Package (Recommended)</h4>
<div class="code-block" data-language="json">
{
<span class="string">"mcpServers"</span>: {
<span class="string">"agr-genomics"</span>: {
<span class="string">"command"</span>: <span class="string">"agr-mcp-server"</span>,
<span class="string">"env"</span>: {
<span class="string">"LOG_LEVEL"</span>: <span class="string">"info"</span>
}
}
}
}
</div>
<h4 style="margin-top: 1.5rem; color: #2980b9;">Option 2: Local Development Setup</h4>
<div class="code-block" data-language="json">
{
<span class="string">"mcpServers"</span>: {
<span class="string">"agr-genomics"</span>: {
<span class="string">"command"</span>: <span class="string">"/usr/local/bin/node"</span>,
<span class="string">"args"</span>: [<span class="string">"/Users/nuin/Projects/alliance/agr-mcp-server-js/src/agr-server-enhanced.js"</span>],
<span class="string">"env"</span>: {
<span class="string">"LOG_LEVEL"</span>: <span class="string">"info"</span>
}
}
}
}
</div>
<p style="margin-top: 1rem; font-size: 0.9rem; color: #7f8c8d;">
<strong>Note:</strong> Use Option 1 after installing the npm package globally.
Use Option 2 for local development or if you cloned the repository.
</p>
</div>
<div class="cards fade-in">
<div class="card">
<span class="card-icon">💻</span>
<h3>CLI Examples</h3>
<div class="code-block" data-language="bash">
<span class="comment"># Natural language queries</span>
alliance <span class="string">"find BRCA1 genes"</span>
alliance <span class="string">"DNA repair genes NOT p53 in human"</span>
<span class="comment"># Performance flags</span>
alliance <span class="string">"PTEN"</span> --fast --limit=5
</div>
</div>
<div class="card">
<span class="card-icon">🧠</span>
<h3>Query Examples</h3>
<ul>
<li>"breast cancer genes in human AND DNA repair NOT p53"</li>
<li>"insulin OR glucose in mouse"</li>
<li>"BRCA1 in human"</li>
<li>"apoptosis genes in zebrafish"</li>
</ul>
</div>
</div>
</div>
</section>
</main>
<!-- Footer -->
<footer class="footer">
<div class="container">
<div class="footer-content">
<div class="footer-section">
<h4>Repository</h4>
<p>agr-mcp-server-js</p>
<p>JavaScript implementation</p>
</div>
<div class="footer-section">
<h4>Package</h4>
<p>agr-mcp-server-enhanced</p>
<p>Available on npm</p>
</div>
<div class="footer-section">
<h4>Architecture</h4>
<p>Node.js + MCP protocol</p>
<p>12 specialized tools</p>
</div>
<div class="footer-section">
<h4>Alliance of Genome Resources</h4>
<p>Genomics research platform</p>
<p>Multi-organism support</p>
</div>
</div>
<p style="border-top: 1px solid #34495e; padding-top: 2rem; margin-top: 2rem; color: #95a5a6;">
AGR MCP Server - Professional genomics research tools
</p>
</div>
</footer>
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