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    Provides a Model Context Protocol server for accessing and querying biomedical data from BioThings services, including gene, variant, chemical, and taxon annotations.
    19
    37
    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
    162 PyPI
    45
    MIT
  • F
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    Integrates the miEAA 3.x bioinformatics platform with Claude Desktop, enabling microRNA enrichment analysis, identifier conversion between miRBase versions, and miRNA-precursor transformations through natural language.
    4
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    Exposes the NGS360 bioinformatics platform REST API as MCP tools, enabling AI assistants to manage sequencing runs, projects, workflows, and more through natural language.
    82
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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
  • A
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    An MCP server that connects AI agents to the PEPTOMA open DeSci peptide research platform, enabling peptide sequence analysis, feed search, and peer-review annotations.
    18 npm
    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.
    454 npm
    MIT
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    MCP server for interacting with Galaxy bioinformatics platform, enabling AI assistants to connect to Galaxy instances, search and execute tools, manage workflows, and access other features.
    39
    MIT
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    Provides a natural language interface for scRNA-Seq analysis using the Scanpy library, supporting operations such as data preprocessing, clustering, and visualization. It enables AI agents and clients to perform complex single-cell transcriptomics workflows through the Model Context Protocol.
    26 PyPI
    2
    BSD 3-Clause
  • A
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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.
    339 npm
    MIT
  • A
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    Enables querying NCI Thesaurus and other cancer-research vocabularies served by NCI Enterprise Vocabulary Services, providing codes, synonyms, definitions, and hierarchical relationships via MCP tools.
    639 npm
    MIT
  • A
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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
  • A
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    Enables AI assistants to create, monitor, and manage computational tasks through GA4GH Task Execution Service (TES) functionality. Provides seamless access to TES-compliant services for executing bioinformatics and scientific computing workflows.
    Apache 2.0
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    MCP server for biological protein design, folding, and affinity prediction using Refua tools, with optional support for ADMET, clinical simulation, preclinical planning, wet-lab automation, and more.
    MIT
  • A
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    Reproduces the in-silico toxicological profile of Heracleum sosnowskyi metabolites from Rassabina & Fedorov (2025) using open-source models for LD50 prediction, toxicity classification, chemical space clustering, and synthesis cost estimation.
    MIT
  • F
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    Enables natural language interface for single-cell RNA-Seq analysis using Liana. Supports reading/writing scRNA-Seq data, cell-cell communication analysis, and visualization through circle plots and dotplots.
    1
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  • F
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    Provides a natural language interface for single-cell RNA-Seq analysis using the decoupleR framework. It enables users to perform biological pathway inference, data clustering, and visualization through MCP-compatible AI clients.
    25 PyPI
    4
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  • F
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    Provides a natural language interface for inferring Copy Number Variations (CNVs) from scRNA-Seq data using the infercnvpy framework. It enables users to perform data preprocessing, CNV inference, and visualization through chromosome heatmaps, UMAP, and t-SNE plots.
    2
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  • F
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    Enables protein modeling and design using the Rosetta suite via Docker, including structure refinement, mutation stability analysis, docking, and loop modeling through natural language commands.
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  • F
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    Enables natural language interaction for scRNA-Seq analysis including preprocessing, clustering, and visualization using the CellRank library. It allows users and agents to perform complex genomic data tasks through standard MCP clients and frameworks.
    2
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  • 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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  • F
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    Enables protein structure prediction using the Chai-1 model via Docker, with tools for small peptides, FASTA-based predictions, MSA-enhanced predictions, batch processing, and job management.
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  • A
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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