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% Title page info
\title{AGR MCP Server}
\subtitle{JavaScript Implementation for Genomics Research}
\author{Development Team}
\institute{Alliance of Genome Resources}
\date{\today}
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{\Large \faIcon{dna} \textcolor{agrblue}{JavaScript Implementation} \faIcon{rocket}}
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\begin{document}
\frame{\titlepage}
% Table of Contents
\begin{frame}{Overview}
\begin{enumerate}
\item \textbf{Overview} - AGR MCP Server Features
\item \textbf{Implementation} - JavaScript Architecture
\item \textbf{Technical Features} - Key Capabilities
\item \textbf{Advanced Query Features} - Natural Language Queries
\item \textbf{Architecture} - High-Performance Design
\item \textbf{Live Demo} - Installation \& Usage
\item \textbf{Status \& Future} - Current Status
\end{enumerate}
\end{frame}
\section{Overview}
\begin{frame}{AGR MCP Server Features}
\begin{itemize}
\item \textbf{Enhanced Query Capabilities} \faIcon{search}
\begin{itemize}
\item Natural language queries
\item Boolean logic (AND, OR, NOT)
\item Species filtering
\item Cross-entity search
\end{itemize}
\item \textbf{Robust Architecture} \faIcon{wrench}
\begin{itemize}
\item Node.js implementation
\item Intelligent caching
\item Error recovery with backoff
\item Comprehensive input validation
\end{itemize}
\item \textbf{Multiple Interfaces} \faIcon{terminal}
\begin{itemize}
\item MCP server for Claude Desktop
\item CLI tools for command line
\item Interactive chat interface
\end{itemize}
\end{itemize}
\end{frame}
\section{Implementation}
\begin{frame}{JavaScript Implementation}
\begin{columns}
\begin{column}{0.5\textwidth}
\textbf{Core Improvements} \faIcon{star}
\begin{itemize}
\item \textcolor{agrblue}{Node.js async I/O}
\item \textcolor{agrgreen}{Intelligent caching}
\item \textcolor{orange}{Connection pooling}
\item \textcolor{purple}{Exponential backoff}
\end{itemize}
\end{column}
\begin{column}{0.5\textwidth}
\textbf{Advanced Features} \faIcon{magic}
\begin{itemize}
\item \textcolor{agrblue}{Natural language queries}
\item \textcolor{agrgreen}{Boolean operators}
\item \textcolor{orange}{Multi-entity search}
\item \textcolor{purple}{Real-time monitoring}
\end{itemize}
\end{column}
\end{columns}
\vspace{1em}
\centering
\begin{tikzpicture}
\node[draw, rounded corners, fill=agrblue!20, text width=8cm, align=center] {
\textbf{12 Specialized MCP Tools} \\
for comprehensive genomics research
};
\end{tikzpicture}
\end{frame}
\section{Technical Features}
\begin{frame}{Key Capabilities}
\begin{center}
\begin{tabular}{|l|l|}
\hline
\textbf{Feature} & \textbf{Implementation} \\
\hline
Caching & NodeCache with TTL (5-10 minutes) \\
Rate Limiting & 100 requests/minute per endpoint \\
Error Handling & Exponential backoff retry \\
Input Validation & Gene ID and sequence validation \\
Logging & Structured logging with Pino \\
Monitoring & Cache hit/miss tracking \\
\hline
\end{tabular}
\end{center}
\vspace{1em}
\begin{alertblock}{Architecture Benefits}
\faIcon{cog} Node.js async I/O with connection pooling for efficient API communication
\end{alertblock}
\end{frame}
\section{Advanced Query Features}
\begin{frame}[fragile]{Natural Language Queries}
\textbf{Boolean Logic Support} \faIcon{brain}
\begin{lstlisting}[language=bash]
# Find DNA repair genes excluding p53 in humans
alliance "breast cancer genes in human AND DNA repair NOT p53"
# Result: 6,021 genes (XRCC3, XRCC1, RAD50, ERCC1, etc.)
# Multiple terms with OR
alliance "insulin OR glucose in mouse"
# Result: 28 genes (Insl5, Igfbp7, Irs3, Ide, etc.)
# Species-specific research
alliance "BRCA1 in human"
# Result: 29 human-specific BRCA1-related genes
\end{lstlisting}
\begin{block}{Supported Operators}
\texttt{AND}, \texttt{OR}, \texttt{NOT} + Species filters (\texttt{in human}, \texttt{in mouse}, etc.)
\end{block}
\end{frame}
\begin{frame}[fragile]{Cross-Entity Search}
\textbf{Multi-Dimensional Queries} \faIcon{project-diagram}
\begin{lstlisting}
// Search genes, diseases, and phenotypes simultaneously
{
"tool": "complex_search",
"arguments": {
"query": "insulin resistance genes and diabetes diseases in human",
"limit": 10
}
}
// Advanced faceted search with multiple filters
{
"tool": "faceted_search",
"arguments": {
"genes": ["BRCA1", "BRCA2", "TP53"],
"diseases": ["breast cancer", "ovarian cancer"],
"processes": ["DNA repair", "apoptosis"],
"species": "Homo sapiens"
}
}
\end{lstlisting}
\end{frame}
\section{Architecture}
\begin{frame}{High-Performance Architecture}
\begin{center}
\begin{tikzpicture}[node distance=2cm]
% Main components
\node[draw, rounded corners, fill=agrblue!30] (client) {MCP Client};
\node[draw, rounded corners, fill=agrgreen!30, below of=client] (server) {Enhanced AGR Server};
\node[draw, rounded corners, fill=orange!30, below left of=server] (cache) {NodeCache\\(TTL: 5-10min)};
\node[draw, rounded corners, fill=purple!30, below of=server] (http) {Axios HTTP Client\\(Connection Pooling)};
\node[draw, rounded corners, fill=red!30, below right of=server] (monitor) {Performance\\Monitoring};
\node[draw, rounded corners, fill=agrgray!30, below of=http] (agr) {AGR APIs};
% Connections
\draw[->] (client) -- (server);
\draw[<->] (server) -- (cache);
\draw[<->] (server) -- (http);
\draw[<->] (server) -- (monitor);
\draw[<->] (http) -- (agr);
\end{tikzpicture}
\end{center}
\begin{columns}
\begin{column}{0.5\textwidth}
\textbf{Key Features:}
\begin{itemize}
\item Rate limiting (100 req/min)
\item Automatic retry logic
\item Input validation
\end{itemize}
\end{column}
\begin{column}{0.5\textwidth}
\textbf{Monitoring:}
\begin{itemize}
\item Cache hit/miss ratios
\item API response times
\item Memory usage tracking
\end{itemize}
\end{column}
\end{columns}
\end{frame}
\section{Live Demo}
\begin{frame}{Installation \& Usage}
\textbf{Quick Setup} \faIcon{rocket}
\begin{block}{Option 1: npm Package (Recommended)}
\begin{lstlisting}[language=bash]
# Install globally from npm
npm install -g agr-mcp-server-enhanced
# Available binaries
agr-mcp-server # Main MCP server
agr-mcp-natural # Natural language server
alliance # CLI interface
agr-chat # Interactive chat
\end{lstlisting}
\end{block}
\begin{block}{Claude Desktop Integration}
\begin{lstlisting}
{
"mcpServers": {
"agr-genomics": {
"command": "agr-mcp-server",
"env": { "LOG_LEVEL": "info" }
}
}
}
\end{lstlisting}
\end{block}
\end{frame}
\begin{frame}[fragile]{Live Examples}
\textbf{Real Query Results} \faIcon{dna}
\begin{exampleblock}{PTEN Gene Search}
\begin{lstlisting}[basicstyle=\tiny\ttfamily]
Query: "find PTEN gene"
Results: 61 genes across species
- PTEN (Homo sapiens) - HGNC:9588
- Pten (Mus musculus) - MGI:109583
- Pten (Drosophila) - FB:FBgn0026379
\end{lstlisting}
\end{exampleblock}
\begin{exampleblock}{Complex Boolean Query}
\begin{lstlisting}[basicstyle=\tiny\ttfamily]
Query: "breast cancer genes in human AND DNA repair NOT p53"
Results: 6,021 genes (XRCC3, XRCC1, RAD50, ERCC1...)
Performance: <2 seconds response time
\end{lstlisting}
\end{exampleblock}
\end{frame}
\section{Status \& Future}
\begin{frame}{Current Status}
\begin{columns}
\begin{column}{0.5\textwidth}
\textbf{Available Features} \faIcon{check-circle}
\begin{itemize}
\item \textcolor{agrgreen}{Natural language queries}
\item \textcolor{agrblue}{Boolean search operators}
\item \textcolor{orange}{Multi-entity search}
\item \textcolor{purple}{Comprehensive caching}
\end{itemize}
\end{column}
\begin{column}{0.5\textwidth}
\textbf{Planned Enhancements} \faIcon{lightbulb}
\begin{itemize}
\item JBrowse integration
\item Batch processing
\item Additional model organisms
\item Extended API coverage
\end{itemize}
\end{column}
\end{columns}
\vspace{1em}
\begin{alertblock}{Installation}
\faIcon{download} Available via npm package and Claude Desktop configuration
\end{alertblock}
</frame>
\begin{frame}{Summary}
\begin{center}
{\Huge \faIcon{dna}}
\vspace{1em}
{\Large AGR MCP Server - JavaScript Implementation}
\vspace{2em}
\begin{columns}
\begin{column}{0.5\textwidth}
\textbf{Repository:} \\
\texttt{agr-mcp-server-js}
\vspace{1em}
\textbf{npm Package:} \\
\texttt{agr-mcp-server-enhanced}
\end{column}
\begin{column}{0.5\textwidth}
\textbf{Architecture:} \\
Node.js with MCP protocol
\vspace{1em}
\textbf{Tools Available:} \\
12 specialized MCP tools
\end{column}
\end{columns}
\end{center}
\end{frame}
\end{document}
