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"Running code or executing programming scripts" matching MCP servers:

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    Enables analysis of bulk RNA-seq data using natural language queries, executing R and Python in a Docker container with automatic sample anonymization and privacy controls.
    7
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    Enables bioinformatics analysis through natural language conversations with Claude Desktop, automatically generating and executing Python scripts to produce HTML reports and visualizations.
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    MIT
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    Enables AI assistants to create, monitor, and manage computational tasks through GA4GH Task Execution Service (TES) functionality. Provides seamless access to TES-compliant services for executing bioinformatics and scientific computing workflows.
    Apache 2.0
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    Enables quantum machine learning operations using Qiskit, including executing quantum circuits, computing quantum kernels, training variational quantum classifiers, and evaluating quantum ML models.
    MIT
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    Enables Claude Code to interact with a TACC or SLURM HPC cluster for bioinformatics pipelines, allowing job management, log reading, file browsing, remote script execution, and job submission through natural language.
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    A bridge connecting AI agents to NCBI's PubMed database through the Model Context Protocol, enabling seamless searching, retrieval, and analysis of biomedical literature and data.
    11
    3,327
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    Apache 2.0
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    An MCP server that enables AI coding assistants to interact with Rosetta, PyRosetta, and Biotite for running RosettaScripts, validating XML, translating between Rosetta and Biotite, scoring structures, and querying documentation.
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    MIT
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    Enables AI agents to conversationally interact with genomics research networks for data analysis and discovery across multiple Omics AI Explorer platforms. It provides tools for exploring data collections, examining table schemas, and executing SQL queries against datasets like Viral AI and Neuroscience AI.
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    MIT
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    Enables users to generate volcano plots by submitting jobs with input files and parameters, supporting local or Docker execution.
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    Enables running GROMACS molecular dynamics simulations through natural language, with tools for topology building, solvation, simulation management, and trajectory processing via the Model Context Protocol.
    31
    MIT
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    MCP server for querying the GWAS Catalog (EBI/NHGRI), a curated catalog of genome-wide association studies. It enables AI agents to search and retrieve study data via natural language or direct tool calls.
    4
    MIT
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    This server provides access to InterPro protein family, domain, and functional-site classification data from EBI. It allows querying protein annotations through natural language or direct tool calls.
    4
    MIT
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    An MCP server that enables scRNA-Seq analysis through natural language, providing tools for data preprocessing, clustering, and biological visualization. It supports both predefined function execution and a flexible code mode powered by a Jupyter backend for automated single-cell transcriptomics workflows.
    15
    BSD 3-Clause