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<title>AGR MCP Server - Enhanced JavaScript Implementation</title>
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<!-- Title Slide -->
<section class="title-slide center">
<h1>🧬 AGR MCP Server</h1>
<h2>Enhanced JavaScript Implementation</h2>
<p>Alliance of Genome Resources<br>Model Context Protocol Server</p>
<p><em>Genomics data access for AI assistants and research tools</em></p>
</section>
<!-- What is it? -->
<section>
<h2>What is the AGR MCP Server?</h2>
<div class="highlight">
<strong>A bridge between AI assistants (like Claude) and genomics databases</strong>
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<ul style="font-size: 1.1em; line-height: 1.8;">
<li><strong>Purpose:</strong> Programmatic access to Alliance of Genome Resources data</li>
<li><strong>Protocol:</strong> Model Context Protocol (MCP) by Anthropic</li>
<li><strong>Language:</strong> JavaScript/Node.js implementation</li>
<li><strong>Target:</strong> Researchers, bioinformaticians, AI tools</li>
</ul>
<div class="architecture-box">
<strong>Claude ↔ MCP Server ↔ AGR APIs ↔ Genomics Databases</strong>
</div>
</section>
<!-- Available Tools -->
<section>
<h2>Available Genomics Tools</h2>
<div class="stats">
<div class="stat">
<div class="stat-number">12</div>
<div class="stat-label">MCP Tools</div>
</div>
<div class="stat">
<div class="stat-number">6</div>
<div class="stat-label">Model Organisms</div>
</div>
<div class="stat">
<div class="stat-number">3</div>
<div class="stat-label">Server Variants</div>
</div>
</div>
<div class="tool-grid">
<div class="tool-item"><strong>search_genes</strong><br>Gene search across species</div>
<div class="tool-item"><strong>get_gene_info</strong><br>Detailed gene information</div>
<div class="tool-item"><strong>get_gene_diseases</strong><br>Disease associations</div>
<div class="tool-item"><strong>search_diseases</strong><br>Disease search</div>
<div class="tool-item"><strong>get_gene_expression</strong><br>Expression data</div>
<div class="tool-item"><strong>find_orthologs</strong><br>Cross-species homologs</div>
<div class="tool-item"><strong>blast_sequence</strong><br>BLAST search</div>
<div class="tool-item"><strong>complex_search</strong><br>Natural language queries</div>
<div class="tool-item"><strong>faceted_search</strong><br>Multi-filter search</div>
<div class="tool-item"><strong>get_species_list</strong><br>Supported organisms</div>
<div class="tool-item"><strong>get_cache_stats</strong><br>Performance monitoring</div>
<div class="tool-item"><strong>clear_cache</strong><br>Cache management</div>
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<h2>System Architecture</h2>
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<h4>🏗️ Core Server</h4>
<ul>
<li>Node.js with async I/O</li>
<li>Axios HTTP client</li>
<li>MCP protocol compliance</li>
</ul>
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<div class="feature-item">
<h4>💾 Caching Layer</h4>
<ul>
<li>NodeCache with TTL</li>
<li>5-10 minute cache times</li>
<li>Automatic cleanup</li>
</ul>
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<div class="feature-item">
<h4>🛡️ Error Handling</h4>
<ul>
<li>Exponential backoff retry</li>
<li>Rate limiting (100 req/min)</li>
<li>Input validation</li>
</ul>
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<div class="feature-item">
<h4>📊 Monitoring</h4>
<ul>
<li>Cache hit/miss tracking</li>
<li>Response time monitoring</li>
<li>Structured logging (Pino)</li>
</ul>
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<div class="architecture-box">
<strong>Three Server Variants:</strong><br>
Enhanced (full features) • Simple (basic tools) • Natural Language (conversational)
</div>
</section>
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<section>
<h2>Advanced Query Features</h2>
<h3>🧠 Natural Language Processing</h3>
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<strong>Boolean Operators:</strong> AND, OR, NOT<br>
<strong>Species Filters:</strong> "in human", "in mouse", "in zebrafish"<br>
<strong>Process Detection:</strong> Automatic biological process recognition
</div>
<h3>📝 Query Examples</h3>
<div class="code-block">
<pre>• "breast cancer genes in human AND DNA repair NOT p53"
• "insulin OR glucose in mouse"
• "BRCA1 in human"
• "apoptosis genes NOT p53 in zebrafish"</pre>
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<h3>🔍 Cross-Entity Search</h3>
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Search genes, diseases, phenotypes, and alleles simultaneously with intelligent relationship discovery
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<h2>Installation & Setup</h2>
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<h3>Option 1: npm Package (Recommended)</h3>
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<pre># Install globally
npm install -g agr-mcp-server-enhanced
# Available commands
agr-mcp-server # Main MCP server
agr-mcp-natural # Natural language server
alliance # CLI interface
agr-chat # Interactive chat</pre>
</div>
<h3>Option 2: From Source</h3>
<div class="code-block">
<pre># Clone and setup
git clone https://github.com/nuin/agr-mcp-server-js.git
cd agr-mcp-server-js
npm run setup</pre>
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</section>
<!-- Claude Integration -->
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<h2>Claude Desktop Integration</h2>
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<strong>Configuration file location:</strong><br>
• macOS: <code>~/Library/Application Support/Claude/claude_desktop_config.json</code><br>
• Windows: <code>%APPDATA%/Claude/claude_desktop_config.json</code>
</div>
<div class="code-block">
<pre>{
"mcpServers": {
"agr-genomics": {
"command": "agr-mcp-server",
"env": {
"LOG_LEVEL": "info"
}
}
}
}</pre>
</div>
<div class="highlight">
<strong>After setup:</strong> Restart Claude Desktop completely, then you can ask genomics questions in natural language
</div>
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<!-- Live Demo -->
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<h2>Live Demo Results</h2>
<h3>🧬 PTEN Gene Search</h3>
<div class="demo-output">Query: "find PTEN gene"
🧬 Found 61 genes:
1. PTEN (Homo sapiens) - HGNC:9588
phosphatase and tensin homolog
2. Pten (Mus musculus) - MGI:109583
phosphatase and tensin homolog
3. Pten (Drosophila melanogaster) - FB:FBgn0026379
Phosphatase and tensin homolog
... and 58 more results</div>
<h3>🔬 Complex Boolean Query</h3>
<div class="demo-output">Query: "PTEN tumor suppressor genes in human"
Results: 1,739 human genes with aggregations:
• Species filtering: ✅ Working
• Boolean parsing: ✅ Functional
• Disease categories: 539 cancer genes
• Process filtering: 1,139 response genes</div>
</section>
<!-- CLI Interface -->
<section>
<h2>Command Line Interface</h2>
<h3>🚀 Performance Flags</h3>
<div class="code-block">
<pre>alliance "find PTEN gene" --fast # Quick results
alliance "find PTEN gene" --detailed # Full information
alliance "find PTEN gene" --limit=5 # Limit results
alliance "find PTEN gene" --simple # Use basic server</pre>
</div>
<h3>⚡ Speed Improvements</h3>
<div class="feature-list">
<div class="feature-item">
<h4>Before Optimization</h4>
<ul>
<li>Timeout after 2+ minutes</li>
<li>Fetched all 61 results</li>
<li>Slow JSON-RPC communication</li>
</ul>
</div>
<div class="feature-item">
<h4>After Optimization</h4>
<ul>
<li>10-second timeout limit</li>
<li>Configurable result limits</li>
<li>Improved server selection</li>
</ul>
</div>
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</section>
<!-- Practical Usage -->
<section>
<h2>Practical Research Applications</h2>
<div class="feature-list">
<div class="feature-item">
<h4>🔬 Gene Research</h4>
<ul>
<li>Cross-species gene searches</li>
<li>Disease association lookup</li>
<li>Ortholog identification</li>
</ul>
</div>
<div class="feature-item">
<h4>🧬 Sequence Analysis</h4>
<ul>
<li>BLAST searches</li>
<li>Expression data queries</li>
<li>Phenotype associations</li>
</ul>
</div>
<div class="feature-item">
<h4>💬 Natural Language</h4>
<ul>
<li>Ask questions in plain English</li>
<li>Boolean logic support</li>
<li>Species-specific filtering</li>
</ul>
</div>
<div class="feature-item">
<h4>🔧 Integration</h4>
<ul>
<li>Claude Desktop ready</li>
<li>CLI tools available</li>
<li>Programmatic access</li>
</ul>
</div>
</div>
</section>
<!-- Current Status -->
<section>
<h2>Current Status & Next Steps</h2>
<h3>✅ What's Working</h3>
<ul style="font-size: 1.1em; line-height: 1.8;">
<li>All 12 MCP tools functional</li>
<li>Claude Desktop integration active</li>
<li>Natural language queries working</li>
<li>CLI interface with performance flags</li>
<li>Comprehensive caching and monitoring</li>
</ul>
<h3>🚧 Areas for Improvement</h3>
<ul style="font-size: 1.1em; line-height: 1.8;">
<li>CLI timeout optimization (completed)</li>
<li>Better error messages for failed queries</li>
<li>Documentation for complex query syntax</li>
<li>Integration with JBrowse genome browser</li>
</ul>
<div class="highlight">
<strong>Ready for:</strong> Research use, testing, feedback from genomics community
</div>
</section>
<!-- Questions -->
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<h1 style="color: white;">Questions & Discussion</h1>
<div style="margin-top: 50px; font-size: 1.2em;">
<p><strong>Repository:</strong> agr-mcp-server-js</p>
<p><strong>npm Package:</strong> agr-mcp-server-enhanced</p>
<p><strong>Installation:</strong> npm install -g agr-mcp-server-enhanced</p>
</div>
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<p><em>Ready for testing and feedback from the genomics research community</em></p>
</div>
</section>
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