"Logs of user or system queries" matching MCP servers:

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.

Converts natural language queries into Cypher queries against the NASA GeneLab Knowledge Graph, enabling AI-assisted analysis of spaceflight experiments and their biological effects.

Provides comprehensive access to the UCSC Genome Browser API, enabling queries of genomic data, DNA sequences, gene annotations, variants, and metadata across multiple species and assemblies.

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.

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.

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.

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.

Provides GPU-accelerated scientific computing capabilities including symbolic mathematics, quantum wave mechanics simulations, molecular dynamics, and neural network training through four specialized MCP servers.

Enables querying of the Monarch Initiative biomedical knowledge graph for genes, diseases, phenotypes, and their associations through natural language or direct tool calls.

Annotate variants by with a deep and rich set of data. Can annotate: genetic change, rsID, CAid, HGVS (g./c./p.), protein change.

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.

An MCP server that provides access to the Kyoto Encyclopedia of Genes and Genomes (KEGG) database, offering 30 tools for searching and analyzing biological data like pathways, genes, and compounds. It supports integration with LangChain and Ollama to enable LLMs to interact with comprehensive genomic and chemical datasets.

Enables AI assistants to query VirtualFlyBrain data, run queries, and search for terms related to Drosophila neurobiology.

Enables querying the BOLD Systems global DNA barcode database for specimen records, taxonomy, barcode sequences, and BIN clusters, with keyless access and FASTA-ready output.

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.

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.

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.

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.

Enables AI assistants to clean PDB structures and run initial-stage energy relaxation for biomolecular modeling. It provides a structured workflow for preparing structures before production molecular dynamics or coarse-graining pipelines.

Provides direct SQL access to a locally hosted Reactome database, enabling schema discovery, guarded read-only queries, and ergonomic helpers over the full relational schema.