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    Provides MCP tool adapters for Bioconductor methods like limma, DESeq2, and fgsea, enabling statistical analysis of omics data through containerized R execution. It serves as a bridge between MCP clients and bioinformatics tools for reproducible research workflows.
    Apache 2.0
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    A Model Context Protocol (MCP) server that provides access to the Protein Data Bank (PDB) - the worldwide repository of information about the 3D structures of proteins, nucleic acids, and complex assemblies.
    5
    28
    MIT
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    Enables AI assistants to query antimicrobial resistance data from the NCBI Reference Gene Catalog, NCBI E-utilities and UniProtKB, and optionally screen genomes with a local AMRFinderPlus install. Supports searching genes by drug class or organism, retrieving allele records, fetching sequences and PubMed references, and looking up protein annotations.
    10
    MIT
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    Natural language-driven spatial transcriptomics analysis via MCP. Integrates 60+ methods for preprocessing, visualization, spatial statistics, cell communication, deconvolution, and trajectory analysis.
    20
    194 PyPI
    45
    MIT
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    Enables AI assistants to query genetic variant data, gene constraints, and population genetics information from the gnomAD (Genome Aggregation Database) through its GraphQL API. Supports searching for genes and variants, retrieving constraint scores, analyzing population frequencies, and accessing genomic coverage data.
    9
    10
    MIT
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    Enables searching ENA's public sequencing data by organism, study, platform, country or date, retrieving FASTQ/BAM download URLs and checksums, and discovering available result types and fields.
    146 npm
    MIT
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    Enables searching a manually curated database of stable macromolecular protein complexes by protein or complex name, gene, GO term, or biological process, and fetching individual records by accession to retrieve subunits with UniProt identifiers, biological roles, and stoichiometry. Complements UniProt, IntAct, and STRING, and can be used keyless over a hosted gateway endpoint or run locally over stdio.
    319 npm
    MIT
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    Enables querying and browsing ontologies from the EBI Ontology Lookup Service, including searching for terms, retrieving term details, and navigating ontology hierarchies via natural language.
    125 npm
    MIT
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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.
    294 npm
    MIT
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    Enables AI agents to resolve marine species names to OBIS taxon records, retrieve georeferenced ocean occurrence records with optional date filtering, and pull aggregate statistics such as record counts, contributing datasets, and observed year ranges. Queries the Ocean Biodiversity Information System keylessly over the Pipeworx gateway or as a local stdio server.
    326 npm
    MIT
  • A
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    Enables querying NCBI genome assemblies, gene details with cross-references, and taxonomy trees with per-node assembly and gene counts, providing structured answers about genomes, genes, and taxonomy.
    300 npm
    MIT
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    Enables querying metadata from MyVariant.info, a comprehensive variant annotation database, providing dataset statistics, source information, and build versions.
    296 npm
    MIT
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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.
    ISC
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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.
    18 PyPI
    MIT
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    An MCP server that enables language models to fetch protein information from the UniProt database, including protein details, sequences, functions, and structures.
    MIT
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    Enables searching and retrieving curated mathematical models of biological systems from BioModels, including metadata, source publications, and downloadable model files in SBML, BioPAX, and other formats, with querying by pathway, disease, organism, gene, or author.
    137 npm
    MIT
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    Enables searching and retrieving expert-curated biochemical reactions from the Rhea database by compound name, ChEBI id, EC number, keyword, or Rhea id, returning balanced plain-text reaction equations alongside EC, ChEBI, UniProt, and PubMed cross-references.
    307 npm
    MIT
  • F
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    An advanced integrated MCP server platform that combines 600+ tools and multiple biomedical databases to enable comprehensive information retrieval across molecules, proteins, genes, and diseases for accelerating therapeutic research.
    40
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    Enables querying and retrieving cell line records from the Cellosaurus knowledge base via its REST API, including searching, fetching by accession, and accessing release information.
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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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    Enables AI assistants to search ImmPort immunology studies and subjects, read study data and assay results, look up controlled vocabularies and the data model, and find study files. Supports study comparison, release history lookups, and guided workflows for cross-study analysis.
    9
    37 PyPI
    MIT
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    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
    39 PyPI
    MIT
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    An MCP server for searching and accessing RNA sequencing datasets from the European Nucleotide Archive (ENA), supporting bulk, single-cell, and spatial transcriptomics with advanced filtering and download capabilities.
    11
    1,843 PyPI
    1
    Apache 2.0
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    Enables interaction with the CEDAR metadata repository, including fetching templates, searching BioPortal ontology terms, and managing template instances.
    8
    MIT
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    Enables AI-assisted molecular biology experiment design with tools for qPCR primer design, cloning strategy optimization, TaqMan probe design, and multiplex compatibility analysis.
    6
    1
    MIT
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    An MCP server that enables AI coding assistants to interact with Rosetta, PyRosetta, and Biotite for running RosettaScripts, validating XML, translating between Rosetta and Biotite, scoring structures, and querying documentation.
    19
    83 npm
    19
    MIT