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  • A
    license
    Not graded
    quality
    A
    maintenance
    An embedded MCP server for Cytoscape Desktop that lets AI agents load networks, set active views, and control the desktop application over HTTP.
    8
    BSD 3-Clause
  • A
    license
    Not graded
    quality
    C
    maintenance
    Enables AI agents to control RELION 5.x cryo-EM structure determination software through natural language, providing 23 tools for the complete single-particle analysis pipeline.
    5
    MIT
  • A
    license
    Not graded
    quality
    B
    maintenance
    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.
    21 npm
    MIT
  • F
    license
    Not graded
    quality
    B
    maintenance
    Connects AI agents to a hosted remote MCP endpoint that searches academic papers, verifies references and retraction status, retrieves research datasets, grants, and biological or chemical data, and generates scientific figures across 50+ upstream sources. Supports OAuth sign-in with per-tool credit accounting, structured error reporting, and source attribution for results.
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  • A
    license
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    quality
    C
    maintenance
    Enables AI assistants to query VCF files through MCP tools that summarize variants, identify pathogenic and carrier variants, interpret pharmacogenomic results, and determine APOE status, with web app and Claude Desktop support.
    MIT
  • F
    license
    Not graded
    quality
    D
    maintenance
    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.
    -
  • A
    license
    A
    quality
    A
    maintenance
    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
  • A
    license
    A
    quality
    B
    maintenance
    Enables AI agents to retrieve cited pharmacogenomic and gene-variant information, including drug–gene guidance from CPIC/DPWG and rsID lookups, so responses can quote curated sources instead of relying on memory. A local package also lets users read raw DNA files on their own computer without sending the file data to the remote service.
    2
    MIT
  • A
    license
    A
    quality
    D
    maintenance
    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
  • A
    license
    A
    quality
    C
    maintenance
    Provides read-only access to the ProPaths verified protein interactome, letting AI agents search proteins, retrieve mechanistic interaction details, and explore pathway ontology through MCP tools, resources, and prompts.
    11
    MIT
  • A
    license
    A
    quality
    C
    maintenance
    Enables LLM agents to search biomedical literature, retrieve article details, find related papers, manage caching, and download open-access full texts through MCP with structured, agent-friendly responses.
    5
    Apache 2.0
  • A
    license
    A
    quality
    A
    maintenance
    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
    4,069 npm
    160
    Apache 2.0
  • F
    license
    A
    quality
    C
    maintenance
    An MCP server that gives Claude access to NCBI Datasets v2 — search genome assembly metadata, retrieve taxonomy records, and download data packages without leaving your conversation.
    10
    -
  • A
    license
    A
    quality
    A
    maintenance
    An MCP server that gives AI assistants access to biological and biomedical RDF databases via SPARQL at the RDF Portal, as well as selected REST APIs (NCBI E-utilities, UniProt, ChEMBL, PDB, Reactome, Rhea, MeSH, and more).
    29
    19
    MIT
  • A
    license
    A
    quality
    C
    maintenance
    Enables LLM-powered applications to look up bacterial and archaeal taxonomy, search genomes, browse and navigate the taxonomic tree, and compare genomes or find phylogenetic paths between taxa. It works out of the box with a built-in reference dataset covering major phyla and can be pointed at full Genome Taxonomy Database TSV files for comprehensive queries.
    12
    1
    MIT
  • A
    license
    A
    quality
    C
    maintenance
    Enables AI assistants to submit genomic sequences or NCBI accessions to antiSMASH for secondary metabolite biosynthetic gene cluster analysis, check job status, retrieve and download results, and query server status across bacteria, fungi, and plant servers.
    10
    1
    MIT
  • A
    license
    A
    quality
    C
    maintenance
    Enables users to search rRNA sequences by organism, accession, or taxonomy, retrieve detailed sequence metadata, evaluate probes and primer pairs, and list available databases and taxonomies through MCP tools.
    6
    MIT