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  • FLASK-tools by FLASK-LLNL

    FLASK-toolsofficial

    FLASK-LLNL
    F
    license
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    maintenance
    Provides a collection of MCP servers for computational chemistry tasks including molecular generation and retrosynthesis. Also offers property prediction and molecule pricing capabilities.
    Last updated

  • MOF Tools MCP Server

    liuyuxiang92
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    quality
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    A specialized MCP server for Metal-Organic Framework research that provides tools for database searching, structural optimization, and energy calculations via ASE. It enables scientific workflows by allowing users to interact with MOF data and perform chemical simulations through a standard SSE interface.
    Last updated
    MIT

  • SCMCP

    huang-sh
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    maintenance
    An MCP server that enables single-cell RNA sequencing analysis through natural language, supporting data processing, visualization, and analysis tasks without requiring coding knowledge.
    Last updated
    52
    12
    BSD 3-Clause

  • Scanpy-MCP

    scmcphub
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    Provides a natural language interface for scRNA-Seq analysis using the Scanpy library, supporting operations such as data preprocessing, clustering, and visualization. It enables AI agents and clients to perform complex single-cell transcriptomics workflows through the Model Context Protocol.
    Last updated
    2
    BSD 3-Clause

  • Poiesis MCP Server

    JaeAeich
    A
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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.
    Last updated
    Apache 2.0

  • SCMCP

    scmcphub
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    quality
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    maintenance
    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.
    Last updated
    15
    BSD 3-Clause

  • MCP-GMX-VMD

    egtai
    A
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    quality
    F
    maintenance
    Integrates GROMACS molecular dynamics simulations with VMD visualization, enabling setup, execution, analysis, and 3D visualization of molecular dynamics workflows through natural language.
    Last updated
    19
    MIT

  • Liana-MCP

    scmcphub
    F
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    quality
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    maintenance
    Enables natural language interface for single-cell RNA-Seq analysis using Liana. Supports reading/writing scRNA-Seq data, cell-cell communication analysis, and visualization through circle plots and dotplots.
    Last updated
    1

  • decoupler-MCP

    scmcphub
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    quality
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    maintenance
    Provides a natural language interface for single-cell RNA-Seq analysis using the decoupleR framework. It enables users to perform biological pathway inference, data clustering, and visualization through MCP-compatible AI clients.
    Last updated
    4

  • Infercnv-MCP

    scmcphub
    F
    license
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    quality
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    maintenance
    Provides a natural language interface for inferring Copy Number Variations (CNVs) from scRNA-Seq data using the infercnvpy framework. It enables users to perform data preprocessing, CNV inference, and visualization through chromosome heatmaps, UMAP, and t-SNE plots.
    Last updated
    2

  • cellrank-mcp

    scmcphub
    F
    license
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    quality
    C
    maintenance
    Enables natural language interaction for scRNA-Seq analysis including preprocessing, clustering, and visualization using the CellRank library. It allows users and agents to perform complex genomic data tasks through standard MCP clients and frameworks.
    Last updated
    2