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  • Oh My KEGG MCP

    martinuslee
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    maintenance
    An MCP server that provides access to the Kyoto Encyclopedia of Genes and Genomes (KEGG) database, offering 30 tools for searching and analyzing biological data like pathways, genes, and compounds. It supports integration with LangChain and Ollama to enable LLMs to interact with comprehensive genomic and chemical datasets.
    Last updated
    8
    MIT

  • rnaseq-mcp

    sbarbi-gh
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    quality
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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.
    Last updated
    7

  • Biomart MCP

    jzinno
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    A Model Context Protocol server that interfaces with Biomart databases, allowing models to discover biological datasets, explore attributes/filters, retrieve biological data, and translate between different biological identifiers.
    Last updated
    8
    7
    MIT

  • mcp-ubergraph-query

    twhetzel
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    Enables AI assistants to query the Ubergraph biomedical ontology SPARQL endpoint with tools for custom SPARQL queries, term lookup, search, and hierarchy traversal.
    Last updated
    4
    MIT

  • BioMCP

    genomoncology
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    quality
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    maintenance
    Provides LLMs with structured access to critical biomedical databases including PubTator3 (PubMed/PMC), ClinicalTrials.gov, and MyVariant.info through the Model Context Protocol.
    Last updated
    35
    561
    MIT

  • Enrichr MCP Server

    tianqitang1
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    Enables gene set enrichment analysis using the Enrichr API across hundreds of gene set libraries including Gene Ontology, pathways, diseases, tissues, drugs, and transcription factors. Returns only statistically significant results for interpretation.
    Last updated
    2
    357
    15
    MIT

  • MCP Sequence Simulation Server

    coreymhudson
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    Enables the generation, mutation, and evolution of DNA and protein sequences using various evolutionary models and phylogenetic algorithms. It supports realistic next-generation sequencing read simulation and population-level evolutionary tracking for bioinformatics research and testing.
    Last updated
    6
    BSD 2-Clause "Simplified"

  • Wegene Assistant MCP Server

    xraywu
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    quality
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    maintenance
    Leverages large language models to analyze users' WeGene genetic testing reports, providing access to report data via custom URI schemes and enabling profile and report management through OAuth authentication and API utilization.
    Last updated
    4
    4

  • MCP PubMed Search

    wavelovey
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    license
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    quality
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    maintenance
    Server to search PubMed (PubMed is a free, online database that allows users to search for biomedical and life sciences literature). I have created on a day MCP came out but was on vacation, I saw someone post similar server in your DB, but figured to post mine.
    Last updated
    1
    47
    MIT

  • cBioPortal MCP Server

    pickleton89
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    quality
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    maintenance
    A server that enables AI assistants to interact with cancer genomics data from cBioPortal, allowing users to explore cancer studies, access genomic data, and retrieve mutations and clinical information.
    Last updated
    17
    5
    MIT