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"Executing CLI commands" matching MCP servers:

  • rnaseq-mcp

    sbarbi-gh
    F
    license
    A
    quality
    C
    maintenance
    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

  • BioNext-mcp

    Cherine0205
    A
    license
    A
    quality
    D
    maintenance
    Enables bioinformatics analysis through natural language conversations with Claude Desktop, automatically generating and executing Python scripts to produce HTML reports and visualizations.
    3
    16
    9
    MIT

  • Poiesis MCP Server

    JaeAeich
    A
    license
    -
    quality
    D
    maintenance
    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

  • MCP LAMMPS Server

    Chenghao-Wu
    A
    license
    -
    quality
    F
    maintenance
    A Model Context Protocol server that enables AI assistants to interact with LAMMPS for molecular dynamics simulations through natural language commands.
    14
    Apache 2.0

  • QML-MCP

    des137
    A
    license
    -
    quality
    D
    maintenance
    Enables quantum machine learning operations using Qiskit, including executing quantum circuits, computing quantum kernels, training variational quantum classifiers, and evaluating quantum ML models.
    MIT

  • VepClin-MCP

    shivankvirdi
    F
    license
    -
    quality
    B
    maintenance
    A terminal-based bioinformatics CLI chat tool that integrates Ensembl VEP, NCBI ClinVar, an MCP server layer, and OpenRouter's NVIDIA Nemotron 3 Ultra model to provide variant consequence and clinical significance lookups with clear summaries in a Rich-powered CLI.

  • pymol-cursor-mcp

    truong128
    F
    license
    -
    quality
    D
    maintenance
    Control PyMOL from Cursor via natural language. Enables describing molecular structures and styles in plain language to execute PyMOL commands through XML-RPC.
    1

  • Gigwa-MCP

    gkanogiannis
    A
    license
    A
    quality
    A
    maintenance
    An MCP server that interfaces with Gigwa for genotyping data import, analysis, and audit, enabling users to perform complex workflows through natural language commands.
    29
    Apache 2.0

  • Omics AI MCP Server

    mfiume
    A
    license
    A
    quality
    D
    maintenance
    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.
    6
    1
    MIT

  • fluxforge

    ali-kishk
    A
    license
    B
    quality
    B
    maintenance
    Predicts CRISPR gene dependencies and drug targets by integrating literature, regulatory/PPI networks, and genome-scale metabolic models.
    18
    Apache 2.0

  • PyMOL-MCP

    vrtejus
    A
    license
    -
    quality
    F
    maintenance
    Connects PyMOL to Claude AI through the Model Context Protocol, allowing for conversational structural biology and molecular visualization through natural language commands.
    66
    MIT

  • Rosetta MCP

    MacromNex
    F
    license
    -
    quality
    D
    maintenance
    Enables protein modeling and design using the Rosetta suite via Docker, including structure refinement, mutation stability analysis, docking, and loop modeling through natural language commands.