标题： BioinfoMCP：一个统一平台，在代理生物信息学中实现MCP接口 显示英文标题

标题： BioinfoMCP: A Unified Platform Enabling MCP Interfaces in Agentic Bioinformatics

摘要： 生物信息学工具对于复杂的计算生物学任务至关重要，但其与新兴人工智能代理框架的集成受到不兼容接口、异构输入输出格式和不一致参数约定的阻碍。 模型上下文协议（MCP）为工具与人工智能的通信提供了一个标准化框架，但手动将数百个现有且迅速增长的专业生物信息学工具转换为MCP兼容的服务器既耗时又不可持续。 在此，我们提出了BioinfoMCP，一个由两个组件组成的统一平台：BioinfoMCP Converter，它使用大语言模型从工具文档自动生成稳健的MCP服务器；BioinfoMCP Benchmark，它系统地验证转换后工具在各种计算任务中的可靠性和通用性。 我们展示了一个包含38个MCP转换的生物信息学工具的平台，经过广泛验证，结果显示94.7%的工具成功在三个广泛使用的AI代理平台上执行复杂的工作流程。 通过消除人工智能自动化的技术障碍，BioinfoMCP使用户能够无需大量编程专业知识即可通过自然语言与复杂的生物信息学分析进行交互，为智能、互操作的计算生物学提供了一条可扩展的路径。 显示英文摘要

摘要： Bioinformatics tools are essential for complex computational biology tasks, yet their integration with emerging AI-agent frameworks is hindered by incompatible interfaces, heterogeneous input-output formats, and inconsistent parameter conventions. The Model Context Protocol (MCP) provides a standardized framework for tool-AI communication, but manually converting hundreds of existing and rapidly growing specialized bioinformatics tools into MCP-compliant servers is labor-intensive and unsustainable. Here, we present BioinfoMCP, a unified platform comprising two components: BioinfoMCP Converter, which automatically generates robust MCP servers from tool documentation using large language models, and BioinfoMCP Benchmark, which systematically validates the reliability and versatility of converted tools across diverse computational tasks. We present a platform of 38 MCP-converted bioinformatics tools, extensively validated to show that 94.7% successfully executed complex workflows across three widely used AI-agent platforms. By removing technical barriers to AI automation, BioinfoMCP enables natural-language interaction with sophisticated bioinformatics analyses without requiring extensive programming expertise, offering a scalable path to intelligent, interoperable computational biology.