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    Enables workflow management and Docker image building for Bio-OS platform. Supports WDL workflow submission, validation, and monitoring, along with Docker image building and status tracking for bioinformatics workflows.
    22
    5
    MIT
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    Parses MS-DIAL binary lipidomics outputs and runs standard analyses server-side, returning compact summaries so an LLM can drive full lipidomics analysis without exposing raw matrices.
    77
    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
    278 PyPI
    MIT
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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.
    8
    8
    MIT
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    Enables LLM agents to search curated short-tandem-repeat disease loci and retrieve exact repeat-count ranges, pathogenic motifs in both orientations, interruptions, inheritance, and per-assembly hg19/hg38/T2T coordinates from a pinned, digest-verified snapshot, plus compare a repeat count against the stated ranges. It also exposes capability and snapshot diagnostics so agents can verify provenance and data integrity.
    5
    MIT
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    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
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    Enables AI assistants to search, browse, and retrieve interactive cell images and subcellular location data, including cell types, SVG illustrations, and location details through natural-language tool calls.
    8
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    MIT
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    Enables LLMs to search, retrieve, and analyze Global Catalogue of Metagenomics data—including BioProjects, BioSamples, Runs, MAGs, biome catalogues, taxonomy abundance, functional annotations, and platform statistics—through natural-language MCP tools.
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    MIT
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    Enables AI assistants to search and retrieve prokaryotic names, taxon details, full classifications, and rank-based browsing from the List of Prokaryotic names with Standing in Nomenclature in real time, plus read related information pages.
    7
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    MIT
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    Retrieve genomic data from EGA, ENA, ENCODE, GEO and NCBI, read bounded regions from indexed BAM/CRAM, VCF and bigWig files, and query source-attributed reference evidence. Runs locally with 23 MCP tools. MIT-licensed; research use.
    23
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    MIT
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    Enables AI assistants to query and retrieve microbial nomenclature data from the SeqCode Registry through its public REST API. Provides 18 tools for names, genomes, type genomes, register lists, publications, authors, journals, subjects, strains, and full-text search, with pagination and status filtering.
    18
    1
    MIT
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    Enables searching, retrieving, and downloading protein structure data from the RCSB Protein Data Bank. Supports intelligent protein structure search, comprehensive data retrieval, and multiple file format downloads for bioinformatics research.
    3
    19 PyPI
    MIT
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    Provides programmatic access to AlphaFold protein structure predictions and UniProt data, enabling users to retrieve protein structures, summaries, and annotations through natural language.
    3
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    Provides seamless access to the Protein Data Bank in Europe (PDBe) API and search capabilities, enabling AI clients to query protein structures, perform advanced searches, and retrieve structural biology data.
    60
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    Apache 2.0
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    Enables AI assistants to search, browse, analyze, and export biological pathway data from Reactome through natural language.
    56
    62 npm
    6
    Apache 2.0
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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
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    MIT
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    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.
    17
    6
    MIT
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    Enables querying HIV-1 antibody neutralization potency data (IC50/IC80/ID50) and HIV T-cell epitope and antibody-binding-site records from LANL databases.
    94 npm
    MIT
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    Enables AI agents to resolve scientific names to Taxonomic Serial Numbers, traverse complete taxonomic lineages from kingdom to children, and retrieve vernacular names in all languages from an authoritative US-government taxonomy.
    283 npm
    1
    MIT
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    Enables AI agents to search and retrieve compounds, drugs, diseases, pathways, genes, enzymes, glycans, modules, and KO entries; fetch full parsed flat-file entries by ID; and list database contents through keyless REST tools.
    297 npm
    MIT
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    MCP server for querying the GWAS Catalog (EBI/NHGRI), a curated catalog of genome-wide association studies. It enables AI agents to search and retrieve study data via natural language or direct tool calls.
    127 npm
    MIT
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    Enables querying and retrieving bacterial and viral genomic data, features, antimicrobial resistance, and epitopes from the BV-BRC API using natural language.
    1
    MIT
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    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.
    135 npm
    MIT
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    A Model Context Protocol server providing programmatic access to 3D protein structural data from RCSB PDB, PDBe, and UniProt, enabling search, retrieval, comparison, and analysis of protein structures.
    466 npm
    6
    Apache 2.0
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    Enables users to look up yeast genes/loci, search genes and alleles by free text, and retrieve Gene Ontology annotations from the Saccharomyces Genome Database.
    315 npm
    MIT
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    Enables AI agents to query Human Phenotype Ontology clinical phenotype terms, navigate term hierarchies, and retrieve gene-disease and disease-phenotype annotations through keyless MCP tools.
    115 npm
    MIT
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    Enables AI assistants to generate publication-quality bioinformatics visualizations (volcano plots, PCA, heatmaps, etc.) directly from raw biological data.
    MIT
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    Enables AI agents to query clinical genomics databases, retrieve supporting literature, analyze population genetics, and visualize biological pathways.
    18
    MIT