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  • A
    license
    Not graded
    quality
    B
    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.
    344 npm
    MIT
  • A
    license
    A
    quality
    D
    maintenance
    Enables AI-driven pharmacogenomic analysis by querying structured genetic variant, drug response, and disease risk data. Supports natural language questions about medications, traits, and health risks based on user genome data, with privacy-first local execution.
    16
    16 npm
    12
    MIT
  • A
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    quality
    B
    maintenance
    Enables MCP-compatible AI assistants to look up clinical variants and batch-annotate NGS spreadsheet outputs via ClinVar, gnomAD, and VarSome. Provides tools for variant lookup, Excel inspection, and folder-level batch processing.
    MIT
  • F
    license
    B
    quality
    A
    maintenance
    BioMCP is an open-source MCP server that connects any AI assistant to 15 open bioinformatics databases with zero configuration. It provides 23 tools for literature, sequences, BLAST, structures, enrichment, annotations, genomes, interactions, variants, domains, compounds, and single-cell data.
    73
    14
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  • A
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    Not graded
    quality
    D
    maintenance
    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
  • A
    license
    Not graded
    quality
    B
    maintenance
    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
  • A
    license
    Not graded
    quality
    B
    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
    B
    maintenance
    Enables AI agents to search public cancer genomics studies (TCGA, CPTAC, MSK, and more), fetch full details for individual studies, resolve gene symbols to Entrez ids, and list cancer types. Works keylessly against open cBioPortal data over a hosted MCP endpoint, a local stdio server, or plain HTTP.
    414 npm
    MIT
  • A
    license
    Not graded
    quality
    B
    maintenance
    Enables querying metadata from MyVariant.info, a comprehensive variant annotation database, providing dataset statistics, source information, and build versions.
    383 npm
    MIT
  • A
    license
    Not graded
    quality
    D
    maintenance
    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
  • 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
    C
    maintenance
    Enables MCP clients to annotate and classify single human genetic variants in any notation, returning an auditable points-based ACMG verdict with its criteria, gnomAD frequencies, in-silico predictors, ClinVar data, and per-transcript consequences. It is read-only, requires no account or API key, and keeps answers compact while linking back to the source.
    6
    MIT
  • 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
    A
    maintenance
    Enables AI agents to resolve and cross-reference biological entities such as genes, proteins, and aliases across authoritative databases like HGNC, NCBI Entrez, and UniProt, with confidence scores and source citations.
    16
    2
    Apache 2.0
  • A
    license
    A
    quality
    A
    maintenance
    Enables users to resolve regulatory entities, query and analyze biological interactions, inspect evidence, export reproducible network data, and download official compressed source files on demand through an online-first, read-only service.
    9
    MIT
  • A
    license
    A
    quality
    A
    maintenance
    Reads raw lab-instrument files (microscopy, mass spectrometry, chromatography, flow cytometry, NMR, electrophysiology, spectroscopy, plate readers, qPCR) without vendor software, returning metadata, images, spectra and traces as JSON. It also checks files for damage, runs common analyses, and exports to open formats such as OME-TIFF, OME-Zarr, mzML, Parquet and NWB.
    28
    284 PyPI
    10
    Apache 2.0
  • A
    license
    A
    quality
    A
    maintenance
    ▎ Provides 32 tools for plant-genomics locus lookup across 11 free public backends (Ensembl Plants, Phytozome, UniProtKB, Europe PMC, QuickGO, NCBI BLAST, Gramene, KEGG, STRING-DB, ATTED-II, BAR). Takes a TAIR-style locus plus optional organism and returns gene metadata, functional/pathway annotation, interactions, co-expression, and literature — in single-locus, batch, and cross-source synthesis.
    58
    206 PyPI
    8
    MIT
  • A
    license
    B
    quality
    A
    maintenance
    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
    16 PyPI
    3
    MIT
  • A
    license
    B
    quality
    D
    maintenance
    Enables molecular design and simulation through 45 chemistry tools including pKa calculations, geometry optimization, conformer searches, docking, protein cofolding, and ADMET predictions powered by Rowan's computational chemistry platform.
    41
    24 PyPI
    24
    MIT
  • F
    license
    B
    quality
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    maintenance
    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
    -
  • A
    license
    B
    quality
    C
    maintenance
    Enables reproducible target-disease evidence dossier assembly and validation by replaying frozen Open Targets GraphQL responses and checking citations and structured assertions against deterministic scientific contracts.
    2
    Apache 2.0
  • F
    license
    C
    quality
    B
    maintenance
    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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  • A
    license
    C
    quality
    C
    maintenance
    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
    license
    Not graded
    quality
    B
    maintenance
    Enables searching and retrieving cancer-genomics projects, cases, and genomic data files — including TCGA, TARGET, and CPTAC — via keyless, open-access metadata tools. Supports filtering by primary site, project, or data category, and can route plain-English questions to the right tool automatically.
    469 npm
    MIT
  • A
    license
    Not graded
    quality
    A
    maintenance
    Enables discovery of CPIC gene–drug pairs and guidelines, translation of source-supported diplotypes and allele evidence, and browsing or matching of prescribing recommendations via read-only tools. Data comes from the public CPIC Database API with clinical context from ClinPGx.
    579 npm
    1
    Apache 2.0
  • A
    license
    Not graded
    quality
    C
    maintenance
    Enables looking up drug and molecule data — identifiers such as InChIKey, SMILES, CAS, and ChEMBL IDs, plus measured and computed properties and drug information — across PubChem, ChEMBL, and Wikidata. Every returned value carries its cited source, and it covers small molecules, peptides (including modified and cyclic forms), and conjugates such as antibody–drug conjugates.
    Apache 2.0