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  • A
    license
    Not graded
    quality
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    maintenance
    Enables AI agents to resolve scientific (Latin binomial) names to Open Tree of Life taxon IDs, retrieve full taxonomic details, synonyms, and ancestor lineages, and find the most recent common ancestor of up to 10 taxa within the synthetic tree of life. Runs keylessly over a hosted gateway endpoint or locally via npx.
    53 npm
    MIT
  • A
    license
    Not graded
    quality
    A
    maintenance
    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
  • A
    license
    Not graded
    quality
    D
    maintenance
    Enables querying and retrieving bacterial and viral genomic data, features, antimicrobial resistance, and epitopes from the BV-BRC API using natural language.
    MIT
  • A
    license
    Not graded
    quality
    B
    maintenance
    Enables keyless lookup of marine species and genus names, retrieval of full taxonomic lineages by AphiaID, and common vernacular names across languages via MCP tools.
    78 npm
    MIT
  • A
    license
    A
    quality
    A
    maintenance
    Grounds gene-nomenclature work in the HUGO Gene Nomenclature Committee (HGNC) dataset, enabling resolution of gene symbols and IDs to canonical HGNC identifiers, plus cross-references and batch operations.
    9
    MIT
  • F
    license
    A
    quality
    D
    maintenance
    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
    -
  • A
    license
    A
    quality
    D
    maintenance
    MCP server that exposes the UniProt REST API to LLM clients, enabling search and retrieval of protein data via tools like search_uniprotkb, get_entry, and map_ids.
    7
    MIT
  • A
    license
    A
    quality
    C
    maintenance
    Enables editing and querying of Gene Ontology Causal Activity Models (GO-CAMs) through the Barista API. Supports model creation, individual and fact management, evidence addition, and causal pathway construction for biological knowledge representation.
    18
    BSD 3-Clause
  • A
    license
    A
    quality
    C
    maintenance
    Enables users to search multiple public life-science data repositories (GEO, ENA, CELLxGENE, PRIDE, DataCite) with a single query, returning a unified ranked list of datasets with ontology-expanded terms and per-source error reporting.
    3
    MIT
  • A
    license
    A
    quality
    D
    maintenance
    Converts natural language queries into Cypher queries against the NASA GeneLab Knowledge Graph, enabling AI-assisted analysis of spaceflight experiments and their biological effects.
    12
    3
    BSD 3-Clause
  • A
    license
    A
    quality
    C
    maintenance
    Enables gene set enrichment analysis using the Enrichr API across hundreds of gene set libraries including Gene Ontology, pathways, diseases, tissues, drugs, and transcription factors. Returns only statistically significant results for interpretation.
    2
    14 npm
    15
    MIT
  • A
    license
    A
    quality
    A
    maintenance
    Enables AI-powered genomic variant analysis including variant impact prediction, regulatory element discovery, and batch variant scoring. Currently operates in mock mode as a proof-of-concept awaiting the public release of Google DeepMind's AlphaGenome API.
    24
    38 npm
    2
    MIT
  • A
    license
    A
    quality
    D
    maintenance
    Enables the generation, mutation, and evolution of DNA and protein sequences using various evolutionary models and phylogenetic algorithms. It supports realistic next-generation sequencing read simulation and population-level evolutionary tracking for bioinformatics research and testing.
    6
    BSD 2-Clause "Simplified"
  • F
    license
    A
    quality
    F
    maintenance
    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
    26
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