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    An embedded MCP server for Cytoscape Desktop that lets AI agents load networks, set active views, and control the desktop application over HTTP.
    7
    BSD 3-Clause
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    Enables searching cancer genes and curated variants from CIViC, retrieving associated diseases, therapies, and graded evidence items and assertions for clinical interpretation.
    17 npm
    MIT
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    D
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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.
    MIT
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    A server providing access to NCBI E-utilities API for searching and retrieving data from databases like PubMed, Protein, and Nucleotide.
    11 PyPI
    MIT
  • F
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    Enables in-chat scientific viewers for molecular structures, sequence alignments, and slide images, plus data tools for searching structures, fetching sequences, aligning them, and drafting NGS analysis plans.
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    Enables searching for academic papers and preprints across multiple platforms including Semantic Scholar, arXiv, PubMed, and CrossRef. It provides access to research records, DOI lookups, and journal metadata through a unified interface deployed on Cloudflare Workers.
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    An MCP server that grounds protein research in the UniProt SPARQL endpoint, providing tools for querying proteins, sequences, variants, diseases, and more via intent-named tools and raw SPARQL.
    15
    MIT
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    Enables language models to search biomedical literature, fetch sequences, and follow links across Entrez databases through eleven read-only tools wrapping the nine NCBI Entrez E-utilities. It handles URL building, pacing, redirects, response caps, and API-key redaction so queries can be answered without a browser or scraping.
    11
    MIT
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    Provides direct SQL access to a locally hosted Reactome database, enabling schema discovery, guarded read-only queries, and ergonomic helpers over the full relational schema.
    9
    MIT
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    Guides researchers, including those new to BPP, from raw sequence data to a validated control file that has passed a short test run. Wraps BPP command-line tools without running long analyses itself.
    16
    AGPL 3.0
  • F
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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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